plotMutSigProfile {MesKit} | R Documentation |
plotMutSigProfile
plotMutSigProfile( sig_input, patient.id = NULL, mode = NULL, contribution.type = "relative", use.tumorSampleLabel = FALSE )
sig_input |
Result generated by function |
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'. |
Mutational signature profile of patients
## 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)