tumorHeatmap: Heatmap of exposure vectors from tumor genomes

In oirot/tumorHeatmap: Visual comparison of mutational processes in a set of tumors

Description

'tumorHeatmap' function computes the exposure vectors from an MPF file and plots an heatmap, clustering the different tumor genomes by their similarities in the exposure vectors.

Usage

tumorHeatmap(mpfFilePath,
signatures,
signaturesType=signatureTypes$alexandrov32,
numBases=5,
trDir=TRUE,
enforceUniqueTrDir=TRUE,
refGenome=BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
transcriptAnno=TxDb.Hsapiens.UCSC.hg19.knownGene::
TxDb.Hsapiens.UCSC.hg19.knownGene,
verbose=FALSE,
plot=TRUE)

Arguments

mpfFilePath	(Mandatory) The path of the MPF file from which to load the tumor genomes
signatures	(Mandatory) Either a path to the signature file or a vector can be dircetly an object containing the signatures. The object can be a list of vectors, data frames or matrices. Vectors are used for Alexandrov signatures, data frames or matrices for Shiraishi signatures.
signaturesType	(Optional) A string representing the signature type. A list of the allowd signature types is available as the object 'signatureTypes'. Use alexandrov2 for Alexandrov V2 signatures, alandrov32 for Alexandrov V3.2 ones and shiraishi for Shiraishi signatures. DEFAULT: signatureTypes$alexandrov32
numBases	(Optional) Total number of bases (mutated base and flanking bases) to be used for sequence patterns. Must be odd. Default: 5
trDir	(Mandatory) Specifies whether the transcription direction is taken into account in the signature model. If so, only mutations within genomic regions with a defined transcription direction can be considered. Default: TRUE
enforceUniqueTrDir	(Optional) Used only if trDir is TRUE. If enforceUniqueTrDir is TRUE (default), then mutations which map to a region with multiple overlapping genes with opposing transcription directions will be excluded from the analysis. If FALSE, the transcript direction encountered first in the transcript database (see transcriptAnno) is assigned to the mutation.
refGenome	(Mandatory) The reference genome (BSgenome) needed to extract sequence patterns. Default: BSgenome object for hg19.
transcriptAnno	(Optional) Transcript annotation (TxDb object) used to determine the transcription direction. This is required only if trDir is TRUE. Default: TxDb object for hg19.
verbose	(Optional) Print information about reading and processing the mutation data. Default: TRUE
plot	(Optional) Output the heatmap of the computed exposures vectors. Default: TRUE

Details

Many of the parameters of this function are also described in the function 'readGenomesFromMPF()' and 'decomposeTumorGenomes()' from the package 'decompTumor2Sig' as those functions and package are at the base of this function and many parameteres are passed directly to those functions. A more throughout explanation of the parameters and the functions can be found in their documentation, liked in the see also section.

Value

The exposure vector is returned where row are the samples and the columns represent the different signature used

See Also

[decompTumor2Sig] The links to the documentation of the mentioned functions from the package 'decompTumor2Sig' readGenomesFromMPF decomposeTumorGenomes

Examples

## read breast cancer genomes from Nik-Zainal et al (PMID: 22608084)
gfile <- system.file("extdata", "Nik-Zainal_PMID_22608084-MPF.txt.gz",
    package="decompTumor2Sig"
)

## get the filenames with the shiraishi signatures
sigfiles <- system.file("extdata",
    paste0(
        "Nik-Zainal_PMID_22608084-pmsignature-sig",
        1:4, ".tsv"
    ),
    package="decompTumor2Sig"
)
## compute the exposure vectors and plot the heatmap
exposures <- tumorHeatmap(gfile, sigfiles,
    signaturesType=signatureTypes$shiraishi
)

oirot/tumorHeatmap documentation built on Dec. 22, 2021, 4:17 a.m.