library(isoformExprTutorial)
data(bamFiles)
bamFiles
library(isoformExprTutorial)
data(bamFiles)
bamFiles
promptData(bamFiles)
help(package="GenomicFeatures")
help(exonsBy)
help(transcriptsBy)
help(transcriptsByOverlaps)
transcripts(txdb, names = list(gene_name = "ALDOA"))
help(transcripts)
transcripts(txdb, vals = list(gene_name = "ALDOA"))
transcripts(txdb, vals = list(gene_id = "GeneID::262"))
transcripts(txdb, vals = list(gene_id = "262"))
exons(txdb, vals = list(gene_id = "262"))
org.Hs.egSYMBOL2EG$ALDOA
names(transcripts(txdb, vals = list(gene_id = "262")))
aldoa_gr
aldoa_gr
help(package="Biobase")
tx
tx
args(split)
aldoa_gr
aldoa_vals$tx_id
values(tx)
tx
values(tx)
aldoa_gr
tx
pairs
mean(!is.na(xs))
normal
tumor
length(pairs)
length(tx)
hits
hits
labeledLine <- IRanges:::labeledLine
hits
hits
ranges(pairs)
hit_pairs
selectMethod(setdiff, "CompressedIRangesList)
selectMethod(setdiff, "CompressedIRangesList")
"
selectMethod(setdiff, sig="CompressedIRangesList")
showMethods(setdiff)
mean(compat)
mean(reads_unique)
tabulate(queryHits(compat_hits), queryLength(compat_hits))
sum(reads_unique)
subsetByOverlaps(exonsBy(txdb), aldoa_range)
tx
igis <- TxDb.Hsapiens.BioMart.IGIS
igis <- TxDb.Hsapiens.BioMart.igis
TxDb.Hsapiens.BioMart.igis
library(TxDb.Hsapiens.BioMart.igis)
igis <- TxDb.Hsapiens.BioMart.igis
igis
ucsc_tx <- tx
txdb <- igis
aldoa_gr
aldoa_gr
tx
multisplit(unlist(aldoa_vals$gene_id), aldoa_vals$tx_id)
tx
ucsc_tx
ucsc_tx[[3]]
ucsc_tx[[4]]
ucsc_tx[[5]]
ucsc_tx[[6]]
ucsc_tx[[7]]
ucsc_tx[[8]]
tx[[1]]
tx[[2]]
tx[[3]]
tx[[4]]
tx <- ucsc_tx
tx
tx
mean(reads_unique)
mean(unique)
hits
values(hits)
with(values(hits), any(!compatible & unique))
mean(novel_splices)
sum(novel_splices)
head(tx_keys)
head(splice_keys)
unique(splice_keys[novel_splices])
table(splice_keys[novel_splices])
table(table(splice_keys[novel_splices]))
mean(compatible_strand)
counts
assays
args(mapply)
assays
se
assays
se
args(SummarizedExperiment)
selectMethod("SummarizedExperiment", "list")
selectMethod("SummarizedExperiment", "SimpleList")
selectMethod(colnames, "SummarizedExperiment")
colnames(se)
selectMethod(show, "SummarizedExperiment")
dimnames(se)
selectMethod(dimnames, "SummarizedExperiment")
se
uc_top
uc
uc_top
key2gr(names(nj_table), score = as.integer(nj_table))
args(GRanges)
seqinfo(nj_gr)
seqinfo(splices)
seqinfo(pairs)
seqinfo(elementGaps(reads))
seqinfo(elementGaps(reads))
seqinfo(elementGaps(reads))
GRanges
nj_gr
seqlengths(splices)
splices <- elementGaps(reads)
splices <- elementGaps(reads)
splices <- elementGaps(reads)
splices
splices
seqinfo(splices)
seqinfo(nj_gr)
nj_gr
length(normal_uniq)
length(tumor_uniq)
selectMethod(rep, "Rle")
selectMethod(rep.int, "Rle")
rep(Rle("normal"), 10)
mstack(normal = normal, tumor = tumor)
both <- mstack(normal = normal, tumor = tumor)
values(both)
.stack.ind <- IRanges:::.stack.ind
both <- mstack(normal = normal, tumor = tumor)
both <- mstack(normal = normal, tumor = tumor)
values(both)
system.time(both <- mstack(normal = normal, tumor = tumor))
system.time(both <- mstack(normal = normal, tumor = tumor))
system.time(both <- mstack(normal = normal, tumor = tumor))
both_uniq
known_splices
library(ggbio)
unloadNamespace("ggbio")
library(ggbio)
values(both_splices)
read_track
read_track
both_uniq
options(error=recover)
7
selectMethod(stat_table, "GenomicRanges")
args
gr
data
Q
unloadNamespace("ggbio")
library(ggbio)
7
.fun
warnings()
geom_arch
names(args.res)
sapply(args.res, class)
args.res$data
Q
tumor_uniq_splices
summarizeSplices
normal_uniq_splices
normal_uniq
debug(summarizeSplices)
normal_uniq_splices <- summarizeSplices(normal_uniq)
n
splices
Q
splices(normal)
values(normal)$splices
c
undebug(summarizeSplices)
normal_uniq_splices
debug(summarizeSplices)
n
splices
Q
c
normal_uniq_splices
undebug(summarizeSplices)
both_splices
read_track
tx
uc
read_track
normal_uniq
0
0
options(error=NULL)
both_uniq
options(error=recover)
7
dt
unique(as.character(seqnames(dt)))
selectMethod(stat_coverage, "GRanges")
facets
Q
0
read_track
0
0
0
0
unloadNamespace("ggbio")
unloadNamespace("biovizBase")
library(ggbio)
0
0
20
addSteppings
dt
showMethods(addSteppings)
selectMethod(addSteppings, "GenomicRanges")
obj.lst
obj
11
grl
table(elementLengths(grl))
showMethods(endoapply)
selectMethods(endoapply, "CompressedList")
selectMethod(endoapply, "CompressedList")
IRanges:::updateCompressedList
IRanges:::.updateCompressedList
IRanges:::.CompressedList.list.subscript
debug(IRanges:::.CompressedList.list.subscript)
20
endoapply(obj.lst, function(x) x)
n
k
n
n
n
zeroLengthElt
n
n
kOK
n
IRanges:::.compress.list
obj.lst
Q
0
tx_16 <- keepSeqlevels(tx, "chr16")
tx_16
c
undebug(IRanges:::.CompressedList.list.subscript)
tx_16
keepSeqlevels(tx, character())
0
GRanges()
keepSeqlevels(GRanges(), character())
0
p
args(tracks)
0
elementLengths(tx)
roi
dir()
Sweave("tutorial.Rnw")
aldoa_vals$gene_id
sum(is.na(tx_to_val))
length(unlist(aldoa_vals$gene_id))
length(tx_to_val)
length(unlist(aldoa_vals$tx_id))
values(tx)$gene_id
Sweave("tutorial.Rnw")
novel_splices
novel_splices
Sweave("tutorial.Rnw")
novel_splices
Sweave("tutorial.Rnw")
fisher.test(uc_top)
fisher.test(uc_top)$p.value
Sweave("tutorial.Rnw")
uniq_novel_splices
novel_splices
uniq_splices
tumor_uniq_splices
normal_uniq_splices
splices_flat <- unlist(values(tumor)$splices, use.names=FALSE)
which(start(splices_flat) == 30075827)
which(start(splices_flat) == 30075827 & end(splices_flat) == 30078554)
togroup(values(tumor)$splices)[39]
splices[56]
tumor_splices <- values(tumor)$splices
tumor_splices[56]
tumor_hits
subjectHits(tumor_hits)[queryHits == 56]
subjectHits(tumor_hits)[queryHits(tumor_hits) == 56]
values(tumor_hits)[1:4,]
togroup(values(tumor)$splices)[which(start(splices_flat) == 30075827 & end(splices_flat) == 30078554)]
bad_hits <- tumor_hits[queryHits(tumor_hits) %in% togroup(values(tumor)$splices)[which(start(splices_flat) == 30075827 & end(splices_flat) == 30078554)]]
bad_hits
sum(values(bad_hits)$unique)
splices_flat <- values(tumor_uniq)$splices
splices_flat <- unlist(values(tumor_uniq)$splices)
which(start(splices_flat) == 30075827 & end(splices_flat) == 30078554)
debug(summarizeSplices)
n
summarizeSplices
n
names(splice_table)[!names(splice_table) %in% tx_keys]
splice_summary
which(gr2key(splices_flat) == "chr16:30075514:30075781:+")
togroup(splices_flat)[56]
togroup(splices)[56]
splices[77]
values(tumor_hits)[queryHits(tumor_hits) == 77]
values(tumor_hits)[queryHits(tumor_hits) == 77,]
subjectHits(tumor_hits)[queryHits(tumor_hits) == 77]
tumor[77[
tumor[77]
tumor_uniq[77]
tx[1]
tumor["HWI-ST304R_0124:8:44:6710:199892#TAGCTT"]
which(names(tumor) == "HWI-ST304R_0124:8:44:6710:199892#TAGCTT")
subjectHits(tumor_hits)[queryHits(tumor_hits) == 110]
values(tumor_hits)[queryHits(tumor_hits) == 110,]
hit_pairs <- tumor[110]
hit_tx <- tx[1]
hit_splices <- values(hit_pairs)$splices
hit_splices
setdiff(hit_pairs, hit_tx)
hit_pairs <- ranges(hit_pairs)
hit_splices <- ranges(hit_splices)
hit_tx <- ranges(hit_tx)
setdiff(hit_pairs, hit_tx)
tx_within
compatible
compatible
tumor_compat_hits <- tumor_hits[values(tumor_hits)$compatible]
"HWI-ST304R_0124:8:44:6710:199892#TAGCTT" %in% names(tumor)[queryHits(tumor_compat_hits)]
findIsoformOverlaps
Q
Sweave("tutorial.Rnw")
uniq_novel_splices
uniq_splices
novel_splices
uniq_novel_splices
values(uniq_novel_splices)$novel
plot.new()
plot(1:10)
dev.off()
dev.new()
scale_color_discrete
scale_color_brewer
novel_track
 as.list(novel_track)
str(novel_track)
str(novel_track$scales)
scale_color_discrete
scale_color_discrete(c("deepskyblue3", "red"))
novel_track
help(scale_color_discrete)
novel_track
ans
ans
values(ans)
values(ans)
tx[1]
tx[2]
length(tx)
tx[4]
Sweave("tutorial.Rnw")
fisher.test(uc_top)
str(fisher.test(uc_top))
fisher.test(uc_top)$estimate
summary(uc_test)
Sweave("tutorial.Rnw")
Sweave("tutorial.Rnw")
tx
tx[[1]]
tx[[2]]
tx[[3]]
tx[[4]]
tx[[5]]
sessionInfo()
tx_track
source("http://bioconductor.org/biocLite.R")
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
n
Sweave("tutorial.Rnw")
q()
n
