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MutationContextPlot

Draws mutation context plots for sequencing samples. Samples can be included as an array where each individual file corresponds to a sample or as a single csv file. Inputs should contain the minimal number of columns to minimize memory load.

Version 0.1
Bundle sequencing
Categories Plot
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
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Requires R ; SomaticSignatures (R-package) ; VariantAnnotation (R-package) ; ggplot2 (R-package) ; BSgenome.Hsapiens.UCSC.hg18 (R-package) ; BSgenome.Hsapiens.UCSC.hg19 (R-package) ; BSgenome.Hsapiens.UCSC.hg38 (R-package)
Source files component.xml MutationContextPlot.r
Usage Example with default values

Inputs

Name Type Mandatory Description
array Array<CSV> Optional Array of CSV files containing the mutation information. Array keys are used as sample names.
in CSV Optional CSV file containing mutation information for one or more samples. Must contain columns for mutation locus, reference and alternative alleles, and sample. Columns are defined using 'dataCols' and 'sampleCol' parameters.

Outputs

Name Type Description
plot Latex Latex folder containing the mutation context spectra barplots.

Parameters

Name Type Default Description
build string (no default) Genome build of the sample(s). One of 'hg18', 'hg19' or 'hg38'. This is only used to determine the length of chromosomes so don't worry if your samples have been aligned to the Ensembl version of the reference genome.
dataCols string (no default) Comma-separated list of column names containing the chromosome, locus, reference and alternative allele of the variants. Notice that the order of values is significant and assumed to be 'CHR,LOCUS,ALT,REF'.
sampleBySample boolean true Plot all samples in one plot or every sample in an individual plot. Defaults to individual plots. Ignored if input is an array.
sampleCol string "" Name of the column containing sample names. Ignored if array input is used.

Test cases

Test case Parameters IN
array
IN
in
OUT
plot
case1 properties (missing) in (missing)

dataCols=Chr,Locus,Ref,Alt,
sampleCol=Sample,
build=hg19,
sampleBySample=false

case2 properties array (missing) (missing)

dataCols=Chr,Locus,Ref,Alt,
build=hg19


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