hildaBarplot {HiLDA}R Documentation

Read the raw mutation data with the mutation feature vector format, estimate and plot both mutation signatures and their fractions

Description

Read the raw mutation data with the mutation feature vector format, estimate and plot both mutation signatures and their fractions

Usage

hildaBarplot(inputG, hildaResult, sigOrder = NULL, refGroup,
  sortSampleNum = TRUE, refName = "Control", altName = "Case",
  charSize = 3)

Arguments

inputG

a MutationFeatureData S4 class output by the pmsignature.

hildaResult

a rjags class output by HiLD.

sigOrder

the order of signatures if needed (default: NULL).

refGroup

the samples in the reference group (default: NULL).

sortSampleNum

whether to sort plots by number of mutations (default: TRUE).

refName

the name of reference group (default: Control)

altName

the name of the other group (default: Case)

charSize

the size of the character on the signature plot (default: 3)

Value

a list of a signature plot and a barplot of mutational exposures

Examples


load(system.file("extdata/sample.rdata", package="HiLDA"))
inputFile <- system.file("extdata/hildaLocal.rdata", package="HiLDA")
hildaLocal <- readRDS(inputFile)

hildaBarplot(G, hildaLocal, refGroup=1:4)


[Package HiLDA version 1.2.0 Index]