hildaTest {HiLDA}R Documentation

Apply HiLDA to statistically testing the global difference in burdens of mutation signatures between two groups

Description

Apply HiLDA to statistically testing the global difference in burdens of mutation signatures between two groups

Usage

hildaTest(inputG, numSig, refGroup, useInits = NULL, sigOrder = NULL,
  nIter = 2000, nBurnin = 0, pM1 = 0.5, localTest = TRUE, ...)

Arguments

inputG

a MutationFeatureData S4 class output by the pmsignature.

numSig

an integer number of the number of mutational signatures.

refGroup

the indice indicating the samples in the reference group.

useInits

a EstimatedParameters S4 class output by the pmsignature (default: NULL)

sigOrder

the order of the mutational signatures.

nIter

number of total iterations per chain (default: 2000).

nBurnin

length of burn (default: 0).

pM1

the probability of sampling the null (default: 0.5)

localTest

a logical value (default: TRUE)

...

Other arguments passed on to methods.

Value

the output jags file

Examples


load(system.file("extdata/sample.rdata", package="HiLDA"))

## with initial values
hildaLocal <- hildaTest(inputG=G, numSig=3, refGroup=1:4, nIter=1000,
localTest=TRUE)
hildaGlobal <- hildaTest(inputG=G, numSig=3, refGroup=1:4, nIter=1000,
localTest=FALSE)


[Package HiLDA version 1.6.0 Index]