Contents

1 Installation

To install this package, start R (version “4.2”) and enter:

# Install via BioConductor
if (!require("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("katdetectr")

# or the latest version
BiocManager::install("katdetectr", version = "devel")

# or from github
devtools::install_github("https://github.com/ErasmusMC-CCBC/katdetectr")

After installation, you can load the package with:

library(katdetectr)

2 Introduction

katdetectr is an R package for the detection, characterization and visualization of localized hypermutated regions, often referred to as kataegis.

The general workflow of katdetectr can be summarized as follows:

  1. Import of genomic variants; VCF, MAF or VRanges objects.
  2. Detection of kataegis foci.
  3. Visualization of segmentation and kataegis foci.

Please see the Application Note (under submission) for additional background and details of katdetectr. The application note also contains a section regarding the performance of katdetectr and other kataegis detection packages: maftools, ClusteredMutations, SeqKat, kataegis, and SigProfilerClusters.

We have made katdetectr available on BioConductor as this insures reliability, and operability on common operating systems (Linux, Mac, and Windows). We designed katdetectr such that it fits well in the BioConductor ecosystem which allows katdetectr to be used easily in combination with other BioConductor packages and analysis pipelines.

Below, the katdetectr workflow is performed in a step-by-step manner on publicly-available datasets that are included within this package.

2.1 Importing genomic variants

Genomic variants from multiple common data-formats (VCF/MAF and VRanges objects) can be imported into katdetectr.

# Genomic variants stored within the VCF format.
pathToVCF <- system.file(package = "katdetectr", "extdata/CPTAC_Breast.vcf")

# Genomic variants stored within the MAF format.
pathToMAF <- system.file(package = "katdetectr", "extdata/APL_primary.maf")

# In addition, we can generate synthetic genomic variants including kataegis foci using generateSyntheticData().
# This functions returns a VRanges object.
syntheticData <- generateSyntheticData(nBackgroundVariants = 2500, nKataegisFoci = 1)

2.2 Detection of kataegis foci

Using detectKataegis(), we can employ changepoint detection to detect distinct clusters of varying intermutation distance (IMD), mutation rate and size.

Imported genomic variant data can contain either single or multiple samples, in the latter case records can be aggregated by setting aggregateRecords = TRUE. Overlapping genomic variants (e.g., an InDel and SNV) are reduced into a single record.

From the genomic variants data the IMD is calculated. Following, changepoint analysis is performed on the IMD of the genomic variants which results in segments. Lastly, a segment is labelled as kataegis foci if the segment fits the following parameters: minSizeKataegis = 6 and IMDcutoff = 1000.

# Detect kataegis foci within the given VCF file.
kdVCF <- detectKataegis(genomicVariants = pathToVCF)

# # Detect kataegis foci within the given MAF file.
# As this file contains multiple samples, we set aggregateRecords = TRUE.
kdMAF <- detectKataegis(genomicVariants = pathToMAF, aggregateRecords = TRUE)

# Detect kataegis foci within the synthetic data.
kdSynthetic <- detectKataegis(genomicVariants = syntheticData)

All relevant input and subsequent results are stored within KatDetect objects. Using summary(), show() and/or print(), we can generate overviews of these KatDetect object(s).

summary(kdVCF)
## Sample name:                                 CPTAC 
## Total number of genomic variants:            3684 
## Total number of putative Kataegis foci:      9 
## Total number of variants in a Kataegis foci: 133
print(kdVCF)
## Sample name:                                 CPTAC 
## Total number of genomic variants:            3684 
## Total number of putative Kataegis foci:      9 
## Total number of variants in a Kataegis foci: 133
show(kdVCF)
## Class "KatDetect" : KatDetect Object
##                   : S4 class containing 4 slots with names:
##                     kataegisFoci genomicVariants segments info 
## 
## Created on:         Wed Feb 28 17:39:34 2024 
## katdetectr version: 1.5.3 
## 
## summary: 
## --------------------------------------------------------
## Sample name:                                 CPTAC 
## Total number of genomic variants:            3684 
## Total number of putative Kataegis foci:      9 
## Total number of variants in a Kataegis foci: 133
## --------------------------------------------------------
# Or simply:
kdVCF
## Class "KatDetect" : KatDetect Object
##                   : S4 class containing 4 slots with names:
##                     kataegisFoci genomicVariants segments info 
## 
## Created on:         Wed Feb 28 17:39:34 2024 
## katdetectr version: 1.5.3 
## 
## summary: 
## --------------------------------------------------------
## Sample name:                                 CPTAC 
## Total number of genomic variants:            3684 
## Total number of putative Kataegis foci:      9 
## Total number of variants in a Kataegis foci: 133
## --------------------------------------------------------

Underlying data can be retrieved from a KatDetect objects using the following getter functions:

  1. getGenomicVariants() returns: VRanges object. Processed genomic variants used as input for changepoint detection. This VRanges contains the genomic location, IMD, and kataegis status of each genomic variant
  2. getSegments() returns: GRanges object. Contains the segments as derived from changepoint detection. This Granges contains the genomic location, total number of variants, mean IMD and, mutation rate of each segment.
  3. getKataegisFoci() returns: GRanges object. Contains all segments designated as putative kataegis foci according the the specified parameters (minSizeKataegis and IMDcutoff). This Granges contains the genomic location, total number of variants and mean IMD of each putative kataegis foci
  4. getInfo() returns: List object. Contains supplementary information including used parameter settings.
getGenomicVariants(kdVCF)
## VRanges object with 3684 ranges and 5 metadata columns:
##          seqnames    ranges strand         ref              alt     totalDepth
##             <Rle> <IRanges>  <Rle> <character> <characterOrRle> <integerOrRle>
##      [1]     chr1    935222      *           C                A             50
##      [2]     chr1    949608      *           G                A             50
##      [3]     chr1    981131      *           A                G             50
##      [4]     chr1    982722      *           A                G             50
##      [5]     chr1   1164015      *           C                A             50
##      ...      ...       ...    ...         ...              ...            ...
##   [3680]     chrX 153594977      *           G                A             50
##   [3681]     chrX 153627839      *           C                T             50
##   [3682]     chrX 153629155      *           A                G             50
##   [3683]     chrX 153668757      *           G                A             50
##   [3684]     chrX 153764217      *           C                T             50
##                refDepth       altDepth   sampleNames softFilterMatrix | revmap
##          <integerOrRle> <integerOrRle> <factorOrRle>         <matrix> | <list>
##      [1]             20             30         CPTAC                  |      1
##      [2]             20             30         CPTAC                  |      2
##      [3]             20             30         CPTAC                  |      3
##      [4]             20             30         CPTAC                  |      4
##      [5]             20             30         CPTAC                  |      5
##      ...            ...            ...           ...              ... .    ...
##   [3680]             20             30         CPTAC                  |   3683
##   [3681]             20             30         CPTAC                  |   3684
##   [3682]             20             30         CPTAC                  |   3685
##   [3683]             20             30         CPTAC                  |   3686
##   [3684]             20             30         CPTAC                  |   3687
##          variantID       IMD segmentID putativeKataegis
##          <integer> <integer> <integer>        <logical>
##      [1]         1    935222         1            FALSE
##      [2]         2     14386         1            FALSE
##      [3]         3     31523         1            FALSE
##      [4]         4      1591         1            FALSE
##      [5]         5    181293         1            FALSE
##      ...       ...       ...       ...              ...
##   [3680]      3680       442         5            FALSE
##   [3681]      3681     32862         6            FALSE
##   [3682]      3682      1316         6            FALSE
##   [3683]      3683     39602         6            FALSE
##   [3684]      3684     95460         7            FALSE
##   -------
##   seqinfo: 23 sequences from an unspecified genome; no seqlengths
##   hardFilters: NULL
getSegments(kdVCF)
## GRanges object with 452 ranges and 8 metadata columns:
##         seqnames              ranges strand | segmentID totalVariants
##            <Rle>           <IRanges>  <Rle> | <numeric>     <numeric>
##     [1]     chr1           1-3389727      * |         1            11
##     [2]     chr1     3389728-3428608      * |         2             4
##     [3]     chr1    3428609-19199400      * |         3            22
##     [4]     chr1   19199401-19203725      * |         4             4
##     [5]     chr1   19203726-19635011      * |         5             8
##     ...      ...                 ...    ... .       ...           ...
##   [448]     chrX 153577919-153594977      * |         5             6
##   [449]     chrX 153594978-153668757      * |         6             3
##   [450]     chrX 153668758-155270560      * |         7             1
##   [451]     chrY          1-59373566      * |         1             0
##   [452]     chrM             1-16571      * |         1             0
##         firstVariantID lastVariantID    meanIMD mutationRate sampleNames
##              <integer>     <integer>  <numeric>    <numeric> <character>
##     [1]              1            11  308157.00  3.24510e-06       CPTAC
##     [2]             12            15    9720.25  1.02878e-04       CPTAC
##     [3]             16            37  716854.18  1.39498e-06       CPTAC
##     [4]             38            41    1081.25  9.24855e-04       CPTAC
##     [5]             42            49   53910.75  1.85492e-05       CPTAC
##     ...            ...           ...        ...          ...         ...
##   [448]           3675          3680    2843.17  3.51720e-04       CPTAC
##   [449]           3681          3683   24593.33  4.06614e-05       CPTAC
##   [450]           3684          3684 1601802.00  6.24297e-07       CPTAC
##   [451]           <NA>          <NA>         NA  0.00000e+00       CPTAC
##   [452]           <NA>          <NA>         NA  0.00000e+00       CPTAC
##         IMDcutoffValues
##               <numeric>
##     [1]            1000
##     [2]            1000
##     [3]            1000
##     [4]            1000
##     [5]            1000
##     ...             ...
##   [448]            1000
##   [449]            1000
##   [450]            1000
##   [451]            1000
##   [452]            1000
##   -------
##   seqinfo: 25 sequences from an unspecified genome; no seqlengths
getKataegisFoci(kdVCF)
## GRanges object with 9 ranges and 7 metadata columns:
##       seqnames              ranges strand |    fociID sampleNames totalVariants
##          <Rle>           <IRanges>  <Rle> | <integer> <character>     <numeric>
##   [1]     chr3   58108856-58111467      * |         1       CPTAC             7
##   [2]     chr6   32489708-32489949      * |         2       CPTAC            13
##   [3]     chr6   32632598-32632770      * |         3       CPTAC             8
##   [4]     chr6 151669875-151674326      * |         4       CPTAC             7
##   [5]     chr8 144991205-144999107      * |         5       CPTAC            25
##   [6]    chr11   62285208-62298597      * |         6       CPTAC            25
##   [7]    chr14 105405599-105419557      * |         7       CPTAC            23
##   [8]    chr15   86122654-86124712      * |         8       CPTAC             6
##   [9]    chr19     4510560-4513559      * |         9       CPTAC            19
##       firstVariantID lastVariantID   meanIMD IMDcutoff
##            <numeric>     <integer> <numeric> <numeric>
##   [1]            782           788  435.1667      1000
##   [2]           1251          1263   20.0833      1000
##   [3]           1273          1280   24.5714      1000
##   [4]           1358          1364  741.8333      1000
##   [5]           1659          1683  329.2500      1000
##   [6]           2112          2136  557.8750      1000
##   [7]           2591          2613  634.4545      1000
##   [8]           2687          2692  411.6000      1000
##   [9]           3139          3157  166.6111      1000
##   -------
##   seqinfo: 25 sequences from an unspecified genome; no seqlengths
getInfo(kdVCF)
## $sampleName
## [1] "CPTAC"
## 
## $totalGenomicVariants
## [1] 3684
## 
## $totalKataegisFoci
## [1] 9
## 
## $totalVariantsInKataegisFoci
## [1] 133
## 
## $version
## [1] "1.5.3"
## 
## $date
## [1] "Wed Feb 28 17:39:34 2024"
## 
## $parameters
## $parameters$minSizeKataegis
## [1] 6
## 
## $parameters$IMDcutoff
## [1] 1000
## 
## $parameters$test.stat
## [1] "Exponential"
## 
## $parameters$penalty
## [1] "BIC"
## 
## $parameters$pen.value
## [1] 0
## 
## $parameters$method
## [1] "PELT"
## 
## $parameters$minseglen
## [1] 2
## 
## $parameters$aggregateRecords
## [1] FALSE

2.3 Visualization of segmentation and kataegis foci

Per sample, we can visualize the IMD, detected segments and putative kataegis foci as a rainfall plot. In addition, this allows for a per-chromosome approach which can highlight the putative kataegis foci.

rainfallPlot(kdVCF)