plotMutSigProfile {MesKit} | R Documentation

## plotMutSigProfile

### Description

plotMutSigProfile

### Usage

    plotMutSigProfile(
      sig_input,
      patient.id = NULL,
      mode = NULL,
      contribution.type = "relative",
      use.tumorSampleLabel = FALSE
    )

### Arguments

`sig_input` | Result generated by function `fitSignatures` or `triMatrix`.
`patient.id` | Select the specific patients. Default NULL, all patients are included.
`mode` | Type of mutation spectrum. Default NULL. Options:'Original','Reconstructed' or 'Difference'
`contribution.type` | Type of Signature contribution. Default 'realative'. Options:'realative' or 'absolute'.
`use.tumorSampleLabel` | Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'.

### Value

Mutational signature profile of patients

### Examples

    ## input from fitSignatures
    maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit")
    clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit")
    ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit")
    maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")
    phyloTree <- getPhyloTree(maf, patient.id = 'V402')

    ## Load a reference genome.
    library(BSgenome.Hsapiens.UCSC.hg19)

    tri_matrix <- triMatrix(phyloTree)
    fit_out <- fitSignatures(tri_matrix)
    plotMutSigProfile(fit_out)
    ## input from treeMatrix
    plotMutSigProfile(tri_matrix)

[Package MesKit version 1.4.0 Index]