Contents

1 Introduction

Alternative polyadenylation (APA) is one of the most important post-transcriptional regulation mechanisms which occurs in most human genes. APA in a gene can result in altered expression of the gene, which can lead pathological effect to the cells, such as uncontrolled cell cycle and growth. However, there are only limited ways to identify and quantify APA in genes, and most of them suffers from complicated process for library construction and requires large amount of RNAs.

RNA-seq has become one of the most commonly used methods for quantifying genome-wide gene expression. There are massive RNA-seq datasets available publicly such as GEO and TCGA. For this reason, we develop the InPAS algorithm for identifying APA from conventional RNA-seq data.

The workflow for InPAS is:

2 How to

To use InPAS, BSgenome and TxDb object have to be loaded before run.

library(InPAS)
library(BSgenome.Mmusculus.UCSC.mm10)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
path <- file.path(find.package("InPAS"), "extdata")

Users can prepare annotaiton by utr3Annotation with a TxDb and org annotation. The 3UTR annotation prepared by utr3Annotation includes the gaps to next annotation region.

library(org.Hs.eg.db)
samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
            package="GenomicFeatures")
txdb <- loadDb(samplefile)
utr3.sample.anno <- utr3Annotation(txdb=txdb, 
                   orgDbSYMBOL="org.Hs.egSYMBOL")
utr3.sample.anno
## GRanges object with 155 ranges and 7 metadata columns:
##                             seqnames              ranges strand |
##                                <Rle>           <IRanges>  <Rle> |
##      uc001bum.2_5|IQCC|utr3     chr1   32673684-32674288      + |
##    uc001fbq.3_3|S100A9|utr3     chr1 153333315-153333503      + |
##    uc001gde.2_2|LRRC52|utr3     chr1 165533062-165533185      + |
##   uc001hfg.3_15|PFKFB2|utr3     chr1 207245717-207251162      + |
##   uc001hfh.3_15|PFKFB2|utr3     chr1 207252365-207254368      + |
##                         ...      ...                 ...    ... .
##      uc004dsv.3_19|PHF8|CDS     chrX   53964414-53964492      - |
##      uc004dsx.3_15|PHF8|CDS     chrX   53969797-53969835      - |
##     uc004ehz.1_5|ARMCX3|CDS     chrX 100879970-100881109      + |
##    uc004elw.3_6|FAM199X|CDS     chrX 103434289-103434459      + |
##      uc004fmj.1_10|GAB3|CDS     chrX 153906455-153906571      - |
##                                 feature annotatedProximalCP          exon
##                             <character>         <character>   <character>
##      uc001bum.2_5|IQCC|utr3        utr3             unknown  uc001bum.2_5
##    uc001fbq.3_3|S100A9|utr3        utr3             unknown  uc001fbq.3_3
##    uc001gde.2_2|LRRC52|utr3        utr3             unknown  uc001gde.2_2
##   uc001hfg.3_15|PFKFB2|utr3        utr3             unknown uc001hfg.3_15
##   uc001hfh.3_15|PFKFB2|utr3        utr3             unknown uc001hfh.3_15
##                         ...         ...                 ...           ...
##      uc004dsv.3_19|PHF8|CDS         CDS             unknown uc004dsv.3_19
##      uc004dsx.3_15|PHF8|CDS         CDS             unknown uc004dsx.3_15
##     uc004ehz.1_5|ARMCX3|CDS         CDS             unknown  uc004ehz.1_5
##    uc004elw.3_6|FAM199X|CDS         CDS             unknown  uc004elw.3_6
##      uc004fmj.1_10|GAB3|CDS         CDS             unknown uc004fmj.1_10
##                              transcript        gene      symbol truncated
##                             <character> <character> <character> <logical>
##      uc001bum.2_5|IQCC|utr3  uc001bum.2       55721        IQCC     FALSE
##    uc001fbq.3_3|S100A9|utr3  uc001fbq.3        6280      S100A9     FALSE
##    uc001gde.2_2|LRRC52|utr3  uc001gde.2      440699      LRRC52     FALSE
##   uc001hfg.3_15|PFKFB2|utr3  uc001hfg.3        5208      PFKFB2     FALSE
##   uc001hfh.3_15|PFKFB2|utr3  uc001hfh.3        5208      PFKFB2     FALSE
##                         ...         ...         ...         ...       ...
##      uc004dsv.3_19|PHF8|CDS  uc004dsv.3       23133        PHF8     FALSE
##      uc004dsx.3_15|PHF8|CDS  uc004dsx.3       23133        PHF8     FALSE
##     uc004ehz.1_5|ARMCX3|CDS  uc004ehz.1       51566      ARMCX3     FALSE
##    uc004elw.3_6|FAM199X|CDS  uc004elw.3      139231     FAM199X     FALSE
##      uc004fmj.1_10|GAB3|CDS  uc004fmj.1      139716        GAB3     FALSE
##   -------
##   seqinfo: 27 sequences from hg19 genome; no seqlengths

Users can load mm10 and hg19 annotation from pre-prepared data. Here we loaded the prepared mm10 3UTR annotation file.

##step1 annotation
# load from dataset
data(utr3.mm10)

The coverage is calculated from BEDGraph file. The RNA-seq BAM files could be converted to BEDGraph files by bedtools genomecov tool (parameter: -bg -split). PWM and a classifier of polyA signal can be used for adjusting CP sites prediction.

load(file.path(path, "polyA.rds"))
library(cleanUpdTSeq)
data(classifier)
bedgraphs <- c(file.path(path, "Baf3.extract.bedgraph"), 
               file.path(path, "UM15.extract.bedgraph"))
hugeData <- FALSE
##step1 Calculate coverage
coverage <- coverageFromBedGraph(bedgraphs, 
                                 tags=c("Baf3", "UM15"),
                                 genome=BSgenome.Mmusculus.UCSC.mm10,
                                 hugeData=hugeData)
## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string

## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string

## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string

## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string
## we hope the coverage rate of should be greater than 0.75 in the expressed gene.
## which is used because the demo data is a subset of genome.
coverageRate(coverage=coverage,
             txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,
             genome=BSgenome.Mmusculus.UCSC.mm10,
             which = GRanges("chr6", ranges=IRanges(98013000, 140678000)))
## strand information will be ignored.
##      gene.coverage.rate expressed.gene.coverage.rate UTR3.coverage.rate
## Baf3         0.01269026                    0.6583034         0.02334057
## UM15         0.01276385                    0.6621445         0.02353842
##      UTR3.expressed.gene.subset.coverage.rate
## Baf3                                0.8102892
## UM15                                0.8171578
##step2 Predict cleavage sites
CPs <- CPsites(coverage=coverage, 
               genome=BSgenome.Mmusculus.UCSC.mm10,
               utr3=utr3.mm10, 
               search_point_START=200, 
               cutEnd=.2, 
               long_coverage_threshold=3,
               background="10K",
               txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,
               PolyA_PWM=pwm, 
               classifier=classifier,
               shift_range=50,
               step=10)
## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string

## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string
head(CPs)
## GRanges object with 4 ranges and 12 metadata columns:
##                              seqnames              ranges strand |
##                                 <Rle>           <IRanges>  <Rle> |
##      uc009daz.2_10|Mitf|utr3     chr6   98018176-98021358      + |
##      uc009dhz.2_19|Atg7|utr3     chr6 114859343-114860614      + |
##      uc009dmb.2_4|Lrtm2|utr3     chr6 119315133-119317055      - |
##   uc009eet.1_3|BC035044|utr3     chr6 128848044-128850081      - |
##                              annotatedProximalCP          exon  transcript
##                                      <character>   <character> <character>
##      uc009daz.2_10|Mitf|utr3             unknown uc009daz.2_10  uc009daz.2
##      uc009dhz.2_19|Atg7|utr3             unknown uc009dhz.2_19  uc009dhz.2
##      uc009dmb.2_4|Lrtm2|utr3             unknown  uc009dmb.2_4  uc009dmb.2
##   uc009eet.1_3|BC035044|utr3             unknown  uc009eet.1_3  uc009eet.1
##                                     gene      symbol truncated
##                              <character> <character> <logical>
##      uc009daz.2_10|Mitf|utr3       17342        Mitf     FALSE
##      uc009dhz.2_19|Atg7|utr3       74244        Atg7     FALSE
##      uc009dmb.2_4|Lrtm2|utr3      211187       Lrtm2     FALSE
##   uc009eet.1_3|BC035044|utr3      232406    BC035044     FALSE
##                                     fit_value Predicted_Proximal_APA
##                                     <numeric>              <numeric>
##      uc009daz.2_10|Mitf|utr3 12594.6737481599               98018978
##      uc009dhz.2_19|Atg7|utr3 27383.4125399619              114859674
##      uc009dmb.2_4|Lrtm2|utr3 168.550899294257              119316541
##   uc009eet.1_3|BC035044|utr3 128.827479256394              128849128
##                              Predicted_Distal_APA           type utr3start
##                                         <numeric>    <character> <numeric>
##      uc009daz.2_10|Mitf|utr3             98021358 novel proximal  98018276
##      uc009dhz.2_19|Atg7|utr3            114862071   novel distal 114859443
##      uc009dmb.2_4|Lrtm2|utr3            119315133 novel proximal 119316955
##   uc009eet.1_3|BC035044|utr3            128846244   novel distal 128849981
##                                utr3end
##                              <numeric>
##      uc009daz.2_10|Mitf|utr3  98021358
##      uc009dhz.2_19|Atg7|utr3 114860614
##      uc009dmb.2_4|Lrtm2|utr3 119315133
##   uc009eet.1_3|BC035044|utr3 128848044
##   -------
##   seqinfo: 42 sequences from mm10 genome; no seqlengths
##step3 Estimate 3UTR usage
res <- testUsage(CPsites=CPs, 
                 coverage=coverage, 
                 genome=BSgenome.Mmusculus.UCSC.mm10,
                 utr3=utr3.mm10, 
                 method="fisher.exact",
                 gp1="Baf3", gp2="UM15")

##step4 view the results
as(res, "GRanges") 
## GRanges object with 4 ranges and 27 metadata columns:
##              seqnames              ranges strand | annotatedProximalCP
##                 <Rle>           <IRanges>  <Rle> |         <character>
##   uc009daz.2     chr6   98018176-98021358      + |             unknown
##   uc009dhz.2     chr6 114859343-114862071      + |             unknown
##   uc009dmb.2     chr6 119315133-119317055      - |             unknown
##   uc009eet.1     chr6 128846244-128850081      - |             unknown
##               transcript        gene      symbol truncated        fit_value
##              <character> <character> <character> <logical>        <numeric>
##   uc009daz.2  uc009daz.2       17342        Mitf     FALSE 12594.6737481599
##   uc009dhz.2  uc009dhz.2       74244        Atg7     FALSE 27383.4125399619
##   uc009dmb.2  uc009dmb.2      211187       Lrtm2     FALSE 168.550899294257
##   uc009eet.1  uc009eet.1      232406    BC035044     FALSE 128.827479256394
##              Predicted_Proximal_APA Predicted_Distal_APA           type
##                           <numeric>            <numeric>    <character>
##   uc009daz.2               98018978             98021358 novel proximal
##   uc009dhz.2              114859674            114862071   novel distal
##   uc009dmb.2              119316541            119315133 novel proximal
##   uc009eet.1              128849128            128846244   novel distal
##              utr3start   utr3end Baf3_short.form.usage UM15_short.form.usage
##              <numeric> <numeric>             <numeric>             <numeric>
##   uc009daz.2  98018276  98021358      33.5313380764804      1.05214965526127
##   uc009dhz.2 114859443 114860614      520.914790102864      172.152349179872
##   uc009dmb.2 119316955 119315133      8.85786481015595      49.5356159541359
##   uc009eet.1 128849981 128848044      22.6717839771901     0.733409738916531
##              Baf3_long.form.usage UM15_long.form.usage         Baf3_PDUI
##                         <numeric>            <numeric>         <numeric>
##   uc009daz.2      282.82402351953     189.141117177656 0.894007365933945
##   uc009dhz.2      208.02460383653     456.544620517098 0.285379834820432
##   uc009dmb.2     8.53513129879347     70.8126330731015 0.490722314046962
##   uc009eet.1     7.87660311958406     21.9601386481802 0.257840228835381
##                      UM15_PDUI   short.mean.gp1    long.mean.gp1
##                      <numeric>        <numeric>        <numeric>
##   uc009daz.2 0.994467997354577 33.5313380764804  282.82402351953
##   uc009dhz.2 0.726175952044354 520.914790102864  208.02460383653
##   uc009dmb.2 0.588397701216867 8.85786481015595 8.53513129879347
##   uc009eet.1 0.967682015769136 22.6717839771901 7.87660311958406
##                 short.mean.gp2    long.mean.gp2          PDUI.gp1
##                      <numeric>        <numeric>         <numeric>
##   uc009daz.2  1.05214965526127 189.141117177656 0.894007365933945
##   uc009dhz.2  172.152349179872 456.544620517098 0.285379834820432
##   uc009dmb.2  49.5356159541359 70.8126330731015 0.490722314046962
##   uc009eet.1 0.733409738916531 21.9601386481802 0.257840228835381
##                       PDUI.gp2               dPDUI              logFC
##                      <numeric>           <numeric>          <numeric>
##   uc009daz.2 0.994467997354577  -0.100460631420632 -0.153638226758031
##   uc009dhz.2 0.726175952044354  -0.440796117223922  -1.34743575844534
##   uc009dmb.2 0.588397701216867 -0.0976753871699045 -0.261884735309782
##   uc009eet.1 0.967682015769136  -0.709841786933756  -1.90805567602427
##                           P.Value            adj.P.Val
##                         <numeric>            <numeric>
##   uc009daz.2 1.58697962749085e-06 2.11597283665446e-06
##   uc009dhz.2  1.7094761107206e-60  6.8379044428824e-60
##   uc009dmb.2    0.593030861268587    0.593030861268587
##   uc009eet.1 2.63287871984117e-08 5.26575743968234e-08
##   -------
##   seqinfo: 1 sequence from an unspecified genome; no seqlengths
filterRes(res, gp1="Baf3", gp2="UM15",
          background_coverage_threshold=3,
          adj.P.Val_cutoff=0.05, 
          dPDUI_cutoff=0.3, 
          PDUI_logFC_cutoff=0.59)
## GRanges object with 4 ranges and 28 metadata columns:
##              seqnames              ranges strand | annotatedProximalCP
##                 <Rle>           <IRanges>  <Rle> |         <character>
##   uc009daz.2     chr6   98018176-98021358      + |             unknown
##   uc009dhz.2     chr6 114859343-114862071      + |             unknown
##   uc009dmb.2     chr6 119315133-119317055      - |             unknown
##   uc009eet.1     chr6 128846244-128850081      - |             unknown
##               transcript        gene      symbol truncated        fit_value
##              <character> <character> <character> <logical>        <numeric>
##   uc009daz.2  uc009daz.2       17342        Mitf     FALSE 12594.6737481599
##   uc009dhz.2  uc009dhz.2       74244        Atg7     FALSE 27383.4125399619
##   uc009dmb.2  uc009dmb.2      211187       Lrtm2     FALSE 168.550899294257
##   uc009eet.1  uc009eet.1      232406    BC035044     FALSE 128.827479256394
##              Predicted_Proximal_APA Predicted_Distal_APA           type
##                           <numeric>            <numeric>    <character>
##   uc009daz.2               98018978             98021358 novel proximal
##   uc009dhz.2              114859674            114862071   novel distal
##   uc009dmb.2              119316541            119315133 novel proximal
##   uc009eet.1              128849128            128846244   novel distal
##              utr3start   utr3end Baf3_short.form.usage UM15_short.form.usage
##              <numeric> <numeric>             <numeric>             <numeric>
##   uc009daz.2  98018276  98021358      33.5313380764804      1.05214965526127
##   uc009dhz.2 114859443 114860614      520.914790102864      172.152349179872
##   uc009dmb.2 119316955 119315133      8.85786481015595      49.5356159541359
##   uc009eet.1 128849981 128848044      22.6717839771901     0.733409738916531
##              Baf3_long.form.usage UM15_long.form.usage         Baf3_PDUI
##                         <numeric>            <numeric>         <numeric>
##   uc009daz.2      282.82402351953     189.141117177656 0.894007365933945
##   uc009dhz.2      208.02460383653     456.544620517098 0.285379834820432
##   uc009dmb.2     8.53513129879347     70.8126330731015 0.490722314046962
##   uc009eet.1     7.87660311958406     21.9601386481802 0.257840228835381
##                      UM15_PDUI   short.mean.gp1    long.mean.gp1
##                      <numeric>        <numeric>        <numeric>
##   uc009daz.2 0.994467997354577 33.5313380764804  282.82402351953
##   uc009dhz.2 0.726175952044354 520.914790102864  208.02460383653
##   uc009dmb.2 0.588397701216867 8.85786481015595 8.53513129879347
##   uc009eet.1 0.967682015769136 22.6717839771901 7.87660311958406
##                 short.mean.gp2    long.mean.gp2          PDUI.gp1
##                      <numeric>        <numeric>         <numeric>
##   uc009daz.2  1.05214965526127 189.141117177656 0.894007365933945
##   uc009dhz.2  172.152349179872 456.544620517098 0.285379834820432
##   uc009dmb.2  49.5356159541359 70.8126330731015 0.490722314046962
##   uc009eet.1 0.733409738916531 21.9601386481802 0.257840228835381
##                       PDUI.gp2               dPDUI              logFC
##                      <numeric>           <numeric>          <numeric>
##   uc009daz.2 0.994467997354577  -0.100460631420632 -0.153638226758031
##   uc009dhz.2 0.726175952044354  -0.440796117223922  -1.34743575844534
##   uc009dmb.2 0.588397701216867 -0.0976753871699045 -0.261884735309782
##   uc009eet.1 0.967682015769136  -0.709841786933756  -1.90805567602427
##                           P.Value            adj.P.Val      PASS
##                         <numeric>            <numeric> <logical>
##   uc009daz.2 1.58697962749085e-06 2.11597283665446e-06     FALSE
##   uc009dhz.2  1.7094761107206e-60  6.8379044428824e-60      TRUE
##   uc009dmb.2    0.593030861268587    0.593030861268587     FALSE
##   uc009eet.1 2.63287871984117e-08 5.26575743968234e-08      TRUE
##   -------
##   seqinfo: 1 sequence from an unspecified genome; no seqlengths

The process described above can be done in one step.

if(interactive()){
    res <- inPAS(bedgraphs=bedgraphs, tags=c("Baf3", "UM15"), 
              genome=BSgenome.Mmusculus.UCSC.mm10, 
              utr3=utr3.mm10, gp1="Baf3", gp2="UM15",
              txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,
              search_point_START=200,
              short_coverage_threshold=15,
              long_coverage_threshold=3, 
              cutStart=0, cutEnd=.2, 
              hugeData=FALSE,
              shift_range=50,
              PolyA_PWM=pwm, classifier=classifier,
              method="fisher.exact",
              adj.P.Val_cutoff=0.05,
              dPDUI_cutoff=0.3, 
              PDUI_logFC_cutoff=0.59)
}

InPAS can handle single group data.

inPAS(bedgraphs=bedgraphs[1], tags=c("Baf3"), 
      genome=BSgenome.Mmusculus.UCSC.mm10, 
      utr3=utr3.mm10, gp1="Baf3", gp2=NULL,
      txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,
      search_point_START=200,
      short_coverage_threshold=15,
      long_coverage_threshold=3, 
      cutStart=0, cutEnd=.2, 
      hugeData=FALSE, 
      PolyA_PWM=pwm, classifier=classifier,
      method="singleSample",
      adj.P.Val_cutoff=0.05,
      step=10)
## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string

## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string

## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string

## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec =
## dec, : EOF within quoted string
## converged at iteration 1 with logLik: -1835.501 
## converged at iteration 5 with logLik: -838.8306 
## converged at iteration 1 with logLik: -1496.738 
## converged at iteration 13 with logLik: -724.6964 
## converged at iteration 1 with logLik: -997.3022 
## converged at iteration 9 with logLik: -555.5656 
## converged at iteration 1 with logLik: -188.938 
## converged at iteration 24 with logLik: -152.6663 
## converged at iteration 1 with logLik: -462.3804 
## converged at iteration 11 with logLik: -214.1651
## dPDUI is calculated by gp2 - gp1.
## GRanges object with 6 ranges and 22 metadata columns:
##              seqnames              ranges strand | annotatedProximalCP
##                 <Rle>           <IRanges>  <Rle> |         <character>
##   uc009daz.2     chr6   98018176-98021358      + |             unknown
##   uc009dhz.2     chr6 114859343-114862075      + |             unknown
##   uc009die.2     chr6 114860617-114862164      - |             unknown
##   uc009dmb.2     chr6 119315133-119317055      - |             unknown
##   uc009eet.1     chr6 128847265-128850081      - |             unknown
##   uc009eol.1     chr6 140651362-140651622      + |             unknown
##               transcript        gene      symbol truncated        fit_value
##              <character> <character> <character> <logical>        <numeric>
##   uc009daz.2  uc009daz.2       17342        Mitf     FALSE 17843.7079181186
##   uc009dhz.2  uc009dhz.2       74244        Atg7     FALSE 7630.49809358993
##   uc009die.2  uc009die.2      232334       Vgll4     FALSE 10704.6989063837
##   uc009dmb.2  uc009dmb.2      211187       Lrtm2     FALSE  18.635065106255
##   uc009eet.1  uc009eet.1      232406    BC035044     FALSE  227.54183333935
##   uc009eol.1  uc009eol.1       11569       Aebp2      TRUE 204539.698420888
##              Predicted_Proximal_APA Predicted_Distal_APA           type
##                           <numeric>            <numeric>    <character>
##   uc009daz.2               98019022             98021358 novel proximal
##   uc009dhz.2              114860283            114862075   novel distal
##   uc009die.2              114861446            114860617   novel distal
##   uc009dmb.2              119316683            119315133 novel proximal
##   uc009eet.1              128848843            128847265   novel distal
##   uc009eol.1              140651566            140651622 novel proximal
##              utr3start   utr3end
##              <numeric> <numeric>
##   uc009daz.2  98018176  98021358
##   uc009dhz.2 114859343 114860614
##   uc009die.2 114862164 114862092
##   uc009dmb.2 119317055 119315133
##   uc009eet.1 128850081 128848044
##   uc009eol.1 140651362 140651622
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       data2
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      <list>
##   uc009daz.2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        c(473, 460, 457, 450, 442, 436, 433, 435, 435, 431, 421, 420, 422, 423, 422, 422, 416, 417, 416, 417, 412, 416, 421, 424, 418, 408, 417, 406, 414, 415, 411, 402, 403, 393, 362, 348, 295, 266, 232, 230, 228, 224, 219, 216, 208, 206, 206, 205, 196, 196, 198, 197, 197, 199, 200, 197, 209, 213, 212, 211, 210, 213, 203, 204, 209, 207, 215, 216, 216, 215, 215, 215, 215, 206, 206, 206, 203, 205, 205, 206, 205, 203, 199, 199, 195, 193, 189, 196, 194, 194, 201, 203, 204, 202, 209, 211, 214, 220, 220, 220, \n221, 221, 221, 216, 215, 214, 214, 206, 205, 205, 208, 208, 203, 208, 208, 204, 204, 205, 205, 206, 204, 201, 198, 200, 198, 236, 224, 211, 203, 200, 203, 198, 195, 199, 199, 197, 196, 198, 198, 196, 196, 198, 200, 202, 201, 203, 214, 217, 217, 218, 218, 219, 220, 216, 215, 215, 202, 200, 200, 206, 206, 204, 201, 201, 196, 209, 201, 200, 204, 208, 208, 208, 208, 208, 208, 208, 208, 209, 209, 209, 224, 225, 225, 225, 226, 226, 226, 221, 221, 225, 218, 218, 218, 219, 213, 212, 213, 206, 209, 209, 213, \n235, 236, 234, 239, 246, 248, 262, 271, 282, 280, 282, 290, 284, 285, 285, 289, 299, 300, 301, 301, 301, 300, 296, 296, 254, 252, 252, 252, 259, 267, 266, 268, 268, 277, 282, 283, 289, 292, 291, 295, 294, 301, 303, 304, 306, 308, 307, 308, 324, 323, 342, 346, 347, 356, 355, 356, 358, 358, 352, 351, 351, 350, 350, 351, 338, 338, 345, 341, 337, 338, 340, 340, 340, 340, 339, 340, 336, 336, 334, 319, 317, 317, 315, 319, 319, 321, 319, 319, 315, 319, 316, 315, 314, 313, 319, 344, 360, 365, 363, 382, 366, \n366, 361, 362, 353, 356, 342, 334, 323, 322, 319, 313, 317, 325, 327, 323, 317, 324, 321, 321, 317, 321, 325, 325, 325, 329, 332, 328, 334, 323, 323, 322, 328, 320, 317, 318, 317, 317, 313, 323, 319, 313, 310, 318, 319, 306, 306, 306, 288, 288, 276, 273, 274, 268, 268, 269, 266, 266, 266, 266, 265, 266, 266, 269, 271, 270, 264, 264, 271, 270, 268, 274, 274, 287, 287, 286, 286, 286, 286, 286, 292, 293, 294, 291, 292, 290, 290, 291, 294, 292, 292, 294, 293, 300, 302, 275, 258, 250, 251, 229, 226, 225, \n225, 224, 225, 225, 229, 229, 231, 235, 235, 233, 230, 221, 220, 227, 221, 214, 214, 216, 215, 212, 206, 206, 206, 202, 198, 198, 197, 196, 204, 209, 202, 225, 226, 226, 219, 220, 220, 212, 223, 239, 242, 234, 234, 233, 233, 237, 241, 249, 252, 251, 257, 254, 255, 255, 266, 270, 282, 282, 283, 282, 282, 279, 279, 286, 298, 307, 310, 312, 328, 328, 334, 321, 323, 343, 349, 359, 364, 371, 365, 367, 381, 386, 387, 388, 388, 387, 384, 383, 387, 392, 390, 397, 391, 392, 392, 407, 407, 413, 411, 412, 413, \n409, 408, 408, 413, 417, 417, 414, 434, 438, 439, 440, 443, 435, 443, 457, 458, 462, 464, 462, 470, 470, 472, 472, 481, 482, 476, 490, 481, 481, 477, 452, 451, 451, 453, 450, 454, 453, 444, 428, 427, 427, 426, 430, 440, 442, 439, 434, 422, 425, 418, 425, 427, 439, 431, 429, 425, 428, 427, 431, 430, 436, 434, 431, 420, 411, 404, 406, 394, 390, 389, 389, 386, 366, 360, 352, 347, 342, 348, 345, 337, 332, 330, 337, 337, 338, 338, 338, 340, 357, 364, 357, 359, 392, 402, 388, 396, 388, 393, 401, 400, 400, \n400, 399, 393, 390, 394, 395, 381, 377, 376, 378, 380, 386, 382, 368, 367, 362, 361, 361, 355, 356, 373, 375, 368, 366, 375, 362, 361, 360, 366, 371, 385, 384, 383, 384, 379, 379, 377, 377, 376, 380, 403, 397, 391, 403, 404, 406, 417, 417, 425, 420, 417, 407, 413, 415, 428, 447, 451, 450, 453, 466, 467, 467, 467, 469, 466, 466, 460, 462, 457, 464, 468, 468, 469, 469, 479, 501, 502, 509, 502, 502, 504, 497, 498, 497, 499, 502, 502, 478, 472, 465, 459, 425, 418, 421, 413, 413, 407, 400, 405, 405, 405, \n408, 404, 403, 401, 403, 396, 397, 401, 398, 393, 388, 388, 386, 386, 385, 387, 386, 391, 394, 376, 374, 373, 376, 363, 363, 364, 361, 356, 353, 341, 356, 359, 359, 359, 362, 362, 369, 366, 363, 337, 339, 342, 326, 329, 328, 333, 331, 321, 323, 323, 319, 310, 307, 289, 271, 268, 272, 272, 252, 251, 247, 248, 246, 247, 243, 243, 241, 272, 265, 265, 269, 268, 267, 259, 234, 228, 221, 221, 219, 219, 219, 220, 222, 220, 216, 210, 210, 209, 211, 211, 213, 211, 211, 215, 215, 215, 215, 210, 210, 211, 207, \n207, 210, 208, 205, 206, 205, 205, 205, 205, 204, 203, 209, 209, 210, 208, 218, 232, 231, 236, 240, 262, 292, 298, 297, 321, 320, 322, 321, 316, 303, 301, 299, 304, 303, 304, 299, 316, 318, 318)
##   uc009dhz.2                                                                                                                                                                                                                          c(184, 184, 184, 184, 187, 187, 188, 190, 196, 201, 208, 212, 212, 216, 217, 218, 221, 221, 222, 222, 222, 228, 228, 228, 231, 235, 236, 236, 241, 241, 243, 244, 245, 245, 245, 245, 247, 242, 243, 245, 246, 243, 248, 251, 251, 250, 236, 235, 236, 232, 224, 223, 226, 228, 227, 228, 228, 228, 232, 235, 235, 235, 234, 234, 230, 230, 235, 236, 234, 234, 245, 245, 244, 239, 239, 239, 240, 242, 231, 227, 227, 223, 219, 215, 214, 214, 213, 189, 183, 178, 180, 177, 172, 169, 169, 174, 180, 179, 177, 175, \n177, 180, 180, 183, 180, 181, 181, 181, 176, 173, 168, 168, 170, 168, 168, 171, 172, 174, 174, 175, 181, 177, 177, 182, 181, 178, 178, 184, 187, 187, 185, 186, 185, 187, 201, 201, 198, 203, 202, 198, 196, 193, 188, 186, 188, 188, 190, 190, 189, 188, 186, 188, 188, 187, 194, 194, 197, 199, 199, 198, 198, 205, 212, 213, 211, 211, 205, 206, 206, 206, 195, 209, 207, 206, 207, 207, 208, 206, 206, 209, 209, 208, 212, 216, 234, 234, 232, 235, 238, 248, 246, 251, 256, 255, 261, 257, 248, 247, 246, 244, 242, \n239, 239, 236, 242, 241, 241, 239, 244, 247, 243, 240, 241, 247, 250, 250, 251, 257, 270, 271, 277, 282, 295, 289, 295, 295, 295, 289, 282, 284, 285, 283, 292, 292, 280, 281, 283, 281, 281, 282, 285, 289, 297, 300, 302, 303, 303, 305, 305, 306, 307, 302, 303, 302, 295, 302, 300, 298, 295, 293, 293, 286, 280, 279, 278, 279, 278, 276, 277, 277, 291, 278, 285, 290, 289, 291, 291, 305, 306, 303, 303, 306, 302, 299, 282, 283, 291, 288, 283, 274, 274, 269, 263, 267, 261, 266, 266, 264, 275, 278, 279, 279, \n282, 284, 278, 278, 278, 280, 281, 281, 293, 293, 293, 285, 281, 288, 283, 275, 262, 266, 256, 255, 248, 248, 242, 241, 244, 244, 249, 247, 252, 252, 244, 242, 249, 248, 247, 252, 252, 251, 250, 251, 244, 239, 235, 234, 233, 256, 259, 259, 260, 260, 255, 255, 259, 255, 255, 258, 261, 265, 269, 273, 271, 271, 277, 276, 279, 279, 280, 284, 286, 304, 298, 293, 292, 288, 286, 269, 268, 268, 268, 277, 277, 279, 285, 284, 278, 279, 283, 286, 286, 286, 292, 288, 292, 286, 286, 286, 279, 279, 280, 280, 282, \n280, 286, 289, 288, 292, 285, 286, 283, 287, 285, 285, 300, 289, 289, 290, 290, 289, 288, 290, 285, 287, 286, 287, 284, 287, 281, 283, 277, 278, 279, 281, 298, 300, 307, 302, 310, 315, 331, 330, 329, 329, 329, 335, 338, 313, 315, 318, 316, 316, 320, 320, 316, 314, 313, 312, 308, 304, 300, 303, 303, 303, 298, 298, 295, 295, 293, 289, 276, 257, 256, 256, 256, 256, 256, 257, 267, 267, 268, 256, 256, 255, 248, 247, 245, 244, 240, 236, 236, 237, 231, 231, 231, 231, 228, 228, 224, 218, 218, 220, 219, 219, \n217, 214, 214, 208, 208, 205, 196, 191, 190, 190, 175, 175, 177, 176, 176, 172, 170, 161, 160, 157, 158, 157, 157, 154, 154, 152, 152, 151, 149, 147, 121, 119, 111, 106, 98, 93, 75, 71, 71, 71, 69, 63, 61, 61, 56, 52, 52, 52, 48, 48, 48, 46, 46, 44, 44, 44, 44, 37, 37, 37, 36, 36, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 32, 22, 22, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 20, 20, 20, 21, 21, 21, 21, 19, 19, 17, 20, 16, 16, 25, 25, 25, 24, 25, 25, 27, 27, 27, 28, 27, 28, 28, 29, 33, \n35, 43, 45, 44, 44, 48, 56, 56, 58, 60, 77, 79, 79, 80, 82, 90, 88, 91, 21, 84, 92, 92, 92, 94, 95, 100, 101, 101, 101, 99, 101, 101, 102, 102, 104, 104, 104, 105, 109, 109, 112, 115, 115, 116, 117, 118, 122, 122, 122, 122, 125, 131, 132, 134, 141, 142, 142, 152, 157, 158, 164, 164, 173, 173, 177, 188, 188, 192, 192, 193, 196, 200, 202, 204, 203, 213, 214, 218, 226, 227, 227, 229, 226, 224, 224, 227, 220, 225, 236, 237, 246, 253, 256, 271, 298, 302, 313, 313, 317, 328, 324, 325, 316, 329, 329, 332, \n328, 320, 322, 321, 322, 307, 306, 311, 327, 317, 317, 322, 331, 333, 332, 332, 334, 341, 346, 347, 347, 348, 348, 354, 354, 360, 374, 378, 376, 377, 379, 379, 383, 391, 388, 388, 392, 392, 391, 395, 391, 395, 400, 402, 403, 411, 411, 409, 408, 416, 435, 446, 457, 459, 460, 461, 452, 453, 450, 439, 439, 435, 435, 434, 431, 427, 425, 421, 420, 410, 408, 404, 396, 395, 395, 393, 392, 391, 391, 388, 386, 381, 370, 369, 359, 352, 347, 332, 305, 300, 288, 287, 283, 271, 269, 267, 267, 254, 254, 251, 251, \n251, 248, 247, 245, 243, 241, 237, 223, 221, 221, 215, 206, 204, 204, 204, 201, 193, 187, 180, 180, 179, 179, 173, 173, 167, 152, 148, 148, 147, 145, 144, 136, 128, 128, 126, 122, 121, 121, 116, 116, 112, 107, 105, 101, 87, 86, 86, 80, 69, 53, 32, 16, 11, 4, 6, 16, 17, 20, 22, 22, 24, 24, 29, 36, 36, 38, 42, 45, 45, 45, 49, 49, 50, 57, 59, 59, 59, 60, 60, 60, 60, 60, 60, 61, 62, 63, 70, 70, 70, 70, 73, 73, 73, 73, 79, 83, 85, 86, 99, 99, 99, 100, 100, 101, 109, 109, 109, 113, 114, 119, 124, 128)
##   uc009die.2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             c(76, 76, 76, 76, 76, 86, 86, 90, 90, 91, 94, 97, 102, 103, 106, 109, 125, 126, 128, 128, 128, 128, 129, 132, 132, 132, 133, 133, 134, 136, 143, 143, 143, 144, 156, 156, 158, 159, 169, 169, 172, 172, 172, 172, 173, 173, 175, 175, 175, 175, 178, 183, 183, 186, 186, 189, 190, 191, 191, 191, 191, 191, 191, 191, 191, 192, 193, 193, 195, 195, 195, 195, 195)
##   uc009dmb.2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  c(11, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 13, 14, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 21, 21, 18, 18, 18, 18, 18, 18, 18, 18, 20, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 25, 25, 25, 25, 27, 27, 27, 27, 28, 28, 28, 28, 29, 29, 29, 28, 28, 27, 27, 27, 27, 27, 27, 28, 28, 28, 26, 26, \n26, 26, 26, 26, 26, 24, 24, 24, 24, 22, 21, 18, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 15, 15, 13, 13, 13, 13, 12, 12, 12, 12, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 14, 13, 13, 13, 13, 13, 13, 19, 20, 20, 20, \n20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 19, 17, 17, 17, 17, 17, 17, 18, 20, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 23, 23, 23, 23, 23, 24, 23, 23, 23, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 27, 27, 27, 25, 25, 25, 25, 26, 25, 25, 25, 25, 25, 27, 27, 21, 20, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 22, 22)
##   uc009eet.1 c(22, 22, 22, 22, 22, 21, 21, 21, 22, 22, 22, 22, 20, 20, 20, 19, 19, 19, 19, 19, 19, 21, 25, 25, 25, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 8, 8, 8, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 6, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, \n3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 6, 6, 6, 7, 9, 8, 8, 8, 8, 8, 8, 10, 10, 11, 16, 16, \n24, 24, 25, 26, 26, 27, 27, 26, 26, 26, 26, 30, 30, 30, 30, 30, 34, 34, 34, 40, 40, 40, 40, 41, 42, 42, 42, 42, 42, 42, 42, 42, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 47, 48, 49, 49, 49, 49, 49, 49, 49, 49, 52, 52, 53, 53, 53, 53, 53, 53, 53, 57, 57, 57, 57, 55, 55, 54, 51, 52, 44, 44, 43, 42, 45, 44, 44, 44, 44, 44, 44, 40, 40, 41, 42, 42, 39, 39, 39, 36, 37, 38, 38, 37, 43, 43, \n43, 43, 43, 44, 44, 44, 43, 42, 42, 42, 42, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 53, 53, 57, 57, 57, 60, 60, 60, 62, 62, 62, 68, 68, 68, 68, 68, 70, 70, 70, 70, 70, 69, 68, 67, 67, 67, 68, 69, 69, 69, 69, 67, 67, 62, 62, 62, 61, 60, 60, 60, 56, 56, 56, 56, 56, 57, 57, 55, 54, 54, 55, 55, 55, 52, 52, 52, 52, 53, 53, 53, 56, 56, 55, 54, 54, 53, 55, 56, 53, 52, 51, 51, 51, 44, 45, 46, 46, 46, 48, 48, 48, 48, 48, 50, 51, 52, 47, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 46, 49, 49, 44, \n46, 42, 42, 43, 42, 42, 42, 40, 40, 40, 35, 35, 35, 38, 38, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 35, 34, 34, 36, 36, 44, 44, 44, 44, 44, 44, 46, 47, 47, 48, 48, 50, 50, 50, 49, 49, 49, 50, 50, 49, 49, 49, 49, 49, 49, 49, 48, 48, 48, 45, 47, 48, 48, 48, 48, 46, 45, 48, 48, 48, 48, 48, 48, 47, 46, 48, 48, 46, 46, 46, 46, 48, 46, 45, 44, 44, 44, 44, 42, 42, 42, 42, 42, 42, 42, 42, 42, 39, 39, 39, 37, 37, 37, 36, 34, 37, 37, 37, 37, 37, 36, 36, 36, 33, 33, 33, 33, 33, 33, 34, 34, 35, 35, 35, 35, 35, \n33, 35, 33, 33, 24, 24, 24, 24, 24, 24, 23, 21, 21, 20, 20, 18, 18, 18, 18, 18, 18, 17, 18, 18, 18, 18, 18, 18, 18, 18, 23, 23, 23, 23, 21, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 17, 17, 15, 15, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 13, 12, 12, 12, 12, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 16, 16, 16, 16, 15, 15, 16, 16, \n16, 17, 17, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 13, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 23, 23, 23, 23, 20, 20, 23, 24, 24, 24, 26, 26, 26, 26, 26, 25, 25, 25, 25, 26, 25, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 23, 24, 23, 23, 24, 23, 23, 23, 23, 23, 23, 23, 23, 23, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 25, 25, 25, 25, 28, \n28, 28, 28, 28, 28, 28, 31, 31, 32, 32, 32, 32, 32, 32, 31, 26, 24, 24, 24, 24, 34, 36, 39, 39, 39, 37, 38, 38, 38, 38, 39, 39, 39, 39, 44, 46, 46, 45, 45, 46, 46, 46, 46, 46, 46, 47, 48, 48, 48, 48, 48, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 52, 52, 52, 53, 51, 50, 54, 54, 53, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 57, 57, 57, 57, 57, 56, 57, 57, 57, 57, 57, 57, 57, 57, 54, 54, 54, 54, 54, 54, 54, 51, 51, 53, 58, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 49, 47, 46, 47, 47, 51, \n50, 50, 50, 53, 59, 60, 60, 57, 51, 52, 52, 51, 51, 50, 50, 50, 50, 50, 50, 53, 55, 58, 58, 58, 59, 58, 58, 58, 57, 57, 57, 57, 57, 57, 57, 57, 57, 61, 61, 62, 60, 60, 60, 59, 59, 59, 55, 55, 55, 52, 52, 52, 52, 52, 52, 53, 55, 56, 57, 56, 56, 57, 60, 60, 60, 59, 59, 59, 59, 62, 62, 62, 62, 66, 66, 66, 66, 66, 66, 66, 66, 66, 63, 58, 57, 57, 57, 57, 57, 57, 57, 62, 62, 63, 63, 63, 61, 62, 62, 57, 57, 58, 58, 56, 49, 48, 48, 49, 52, 49, 50, 50, 50, 51, 51, 51, 55, 55, 55, 51, 47, 45, 45, 45, 44, 44, \n45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 43, 43, 42, 43, 47, 50, 50, 50, 50, 50, 50, 51, 51, 51, 51, 51, 51, 51, 52, 50, 50, 47, 47, 47, 46, 43, 45, 45, 45, 45, 45, 45, 42, 42, 42, 42, 40, 41, 41, 41, 41, 41, 41)
##   uc009eol.1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                c(1408, 1412, 1384, 1385, 1398, 1399, 1385, 1408, 1416, 1460, 1513, 1544, 1569, 1623, 1677, 1685, 1700, 1712, 1717, 1726, 1738, 1742, 1754, 1734, 1727, 1685, 1695, 1699, 1709, 1689, 1671, 1728, 1732, 1719, 1727, 1724, 1739, 1744, 1743, 1766, 1756, 1787, 1779, 1819, 1839, 1980, 1995, 1998, 1995, 1990, 1958, 1942, 1928, 1922, 1919, 1930, 1910, 1907, 1895, 1885, 1885, 1886, 1886, 1896, 1884, 1870, 1863, 1825, 1846, 1842, 1825, 1797, 1675, 1668, 1659, 1659, 1657, 1655, 1645, 1635, 1617, 1595, 1577, 1579, \n1578, 1562, 1557, 1536, 1506, 1495, 1486, 1482, 1480, 1488, 1454, 1455, 1435, 1426, 1407, 1387, 1352, 1357, 1352, 1389, 1369, 1363, 1377, 1365, 1376, 1377, 1322, 1315, 1288, 1239, 1174, 1163, 1151, 1137, 1130, 1119, 1128, 1128, 1128, 1141, 1142, 1143, 1155, 1187, 1174, 1182, 1180, 1129, 1125, 1150, 1139, 1129, 1106, 1100, 1096, 1075, 1052, 1017, 992, 957, 942, 765, 755, 761, 765, 767, 769, 771, 776, 787, 788, 773, 772, 767, 760, 760, 756, 755, 753, 743, 743, 742, 740, 742, 710, 707, 699, 694, 689, \n689, 687, 684, 684, 679, 679, 664, 657, 657, 648, 634, 634, 633, 632, 631, 629, 629, 629, 628, 628, 614, 614, 603, 601, 601, 594, 590, 576, 561, 545, 502)
##              Baf3_short.form.usage Baf3_long.form.usage         Baf3_PDUI
##                          <numeric>            <numeric>         <numeric>
##   uc009daz.2      29.6602572856635     283.389388104407 0.905253822444981
##   uc009dhz.2       3.7254488495449     209.978806469604 0.982567268751943
##   uc009die.2        121.8881378455     174.122891566265 0.588231093659866
##   uc009dmb.2      9.22609762692124     9.11798839458414 0.497053294663731
##   uc009eet.1      22.0449523788087     10.3274224192527 0.319019611124456
##   uc009eol.1      1065.98013415893     221.456140350877 0.172013283092553
##                    short.mean        long.mean              PDUI P.Value
##                        <list>           <list>            <list>  <list>
##   uc009daz.2 29.6602572856635 283.389388104407 0.905253822444981       1
##   uc009dhz.2  3.7254488495449 209.978806469604 0.982567268751943       1
##   uc009die.2   121.8881378455 174.122891566265 0.588231093659866       1
##   uc009dmb.2 9.22609762692124 9.11798839458414 0.497053294663731       1
##   uc009eet.1 22.0449523788087 10.3274224192527 0.319019611124456       1
##   uc009eol.1 1065.98013415893 221.456140350877 0.172013283092553       1
##              adj.P.Val     dPDUI      PASS
##                 <list> <numeric> <logical>
##   uc009daz.2         1       NaN     FALSE
##   uc009dhz.2         1       NaN     FALSE
##   uc009die.2         1       NaN     FALSE
##   uc009dmb.2         1       NaN     FALSE
##   uc009eet.1         1       NaN     FALSE
##   uc009eol.1         1       NaN     FALSE
##   -------
##   seqinfo: 1 sequence from an unspecified genome; no seqlengths

3 Session Info

sessionInfo()

R version 3.5.1 Patched (2018-07-12 r74967) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS

Matrix products: default BLAS: /home/biocbuild/bbs-3.8-bioc/R/lib/libRblas.so LAPACK: /home/biocbuild/bbs-3.8-bioc/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] cleanUpdTSeq_1.20.0
[2] e1071_1.7-0
[3] seqinr_3.4-5
[4] BSgenome.Drerio.UCSC.danRer7_1.4.0
[5] org.Hs.eg.db_3.7.0
[6] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4 [7] BSgenome.Mmusculus.UCSC.mm10_1.4.0
[8] BSgenome_1.50.0
[9] rtracklayer_1.42.0
[10] Biostrings_2.50.0
[11] XVector_0.22.0
[12] InPAS_1.14.0
[13] GenomicFeatures_1.34.0
[14] AnnotationDbi_1.44.0
[15] GenomicRanges_1.34.0
[16] GenomeInfoDb_1.18.0
[17] IRanges_2.16.0
[18] S4Vectors_0.20.0
[19] Biobase_2.42.0
[20] BiocGenerics_0.28.0
[21] BiocStyle_2.10.0

loaded via a namespace (and not attached): [1] ProtGenerics_1.14.0 bitops_1.0-6
[3] matrixStats_0.54.0 bit64_0.9-7
[5] RColorBrewer_1.1-2 progress_1.2.0
[7] httr_1.3.1 rprojroot_1.3-2
[9] tools_3.5.1 backports_1.1.2
[11] R6_2.3.0 rpart_4.1-13
[13] Hmisc_4.1-1 DBI_1.0.0
[15] lazyeval_0.2.1 Gviz_1.26.0
[17] colorspace_1.3-2 ade4_1.7-13
[19] nnet_7.3-12 tidyselect_0.2.5
[21] gridExtra_2.3 prettyunits_1.0.2
[23] preprocessCore_1.44.0 curl_3.2
[25] bit_1.1-14 compiler_3.5.1
[27] htmlTable_1.12 DelayedArray_0.8.0
[29] bookdown_0.7 scales_1.0.0
[31] checkmate_1.8.5 stringr_1.3.1
[33] digest_0.6.18 Rsamtools_1.34.0
[35] foreign_0.8-71 rmarkdown_1.10
[37] dichromat_2.0-0 base64enc_0.1-3
[39] pkgconfig_2.0.2 htmltools_0.3.6
[41] ensembldb_2.6.0 limma_3.38.0
[43] htmlwidgets_1.3 rlang_0.3.0.1
[45] rstudioapi_0.8 RSQLite_2.1.1
[47] bindr_0.1.1 BiocParallel_1.16.0
[49] acepack_1.4.1 dplyr_0.7.7
[51] VariantAnnotation_1.28.0 RCurl_1.95-4.11
[53] magrittr_1.5 GenomeInfoDbData_1.2.0
[55] Formula_1.2-3 Matrix_1.2-14
[57] Rcpp_0.12.19 munsell_0.5.0
[59] stringi_1.2.4 yaml_2.2.0
[61] MASS_7.3-51 SummarizedExperiment_1.12.0 [63] zlibbioc_1.28.0 plyr_1.8.4
[65] grid_3.5.1 blob_1.1.1
[67] crayon_1.3.4 lattice_0.20-35
[69] splines_3.5.1 hms_0.4.2
[71] knitr_1.20 pillar_1.3.0
[73] biomaRt_2.38.0 XML_3.98-1.16
[75] glue_1.3.0 evaluate_0.12
[77] biovizBase_1.30.0 latticeExtra_0.6-28
[79] data.table_1.11.8 BiocManager_1.30.3
[81] gtable_0.2.0 purrr_0.2.5
[83] assertthat_0.2.0 ggplot2_3.1.0
[85] xfun_0.4 depmixS4_1.3-5
[87] AnnotationFilter_1.6.0 Rsolnp_1.16
[89] class_7.3-14 survival_2.43-1
[91] truncnorm_1.0-8 tibble_1.4.2
[93] GenomicAlignments_1.18.0 memoise_1.1.0
[95] bindrcpp_0.2.2 cluster_2.0.7-1