triMatrix {MesKit} | R Documentation |
Calculate the frequency of 96 trinucleotide mutation based on somatic SNVs.
triMatrix(phyloTree, patient.id = NULL, level = 2)
phyloTree |
phyloTree or phyloTreeList object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included |
level |
Calculate the frequency of 96 trinucleotide mutatio on different levels. 1: patient-level, 2: tumor-level, 3: sample-level, 4: branch-level, 5: shared pattern (public/shared/private) of each tumor. 6: trunk/branch-level. Default 2. |
The frequency of 96 trinucleotide mutation.
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") ## Load a reference genome. library(BSgenome.Hsapiens.UCSC.hg19) phyloTree <- getPhyloTree(maf, patient.id = 'V402') triMatrix(phyloTree)