mutTrunkBranch {MesKit} | R Documentation |
Summarize and conduct paired Fisher test of mutations of trunk/branches in a phylogenetic tree.
mutTrunkBranch( phyloTree, patient.id = NULL, CT = FALSE, pvalue = 0.05, plot = TRUE )
phyloTree |
phyloTree or phyloTreeList object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included |
CT |
Distinction between C>T at CpG and C>T at other sites. (Default: FALSE). |
pvalue |
Confidence level of the interval for Fisher test. Default 0.05. |
plot |
Logical. (Default: TRUE). |
a list of box plots based on mutational categories
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') mutTrunkBranch(phyloTree, plot = TRUE)