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 1.2.0 Index]