hildaBarplot: Read the raw mutation data with the mutation feature vector...

In USCbiostats/HiLDA: Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

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 HiLDA.
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)

USCbiostats/HiLDA documentation built on Oct. 15, 2021, 10:22 a.m.