hildaTest {HiLDA} | R Documentation |
Apply HiLDA to statistically testing the global difference in burdens of mutation signatures between two groups
hildaTest( inputG, numSig, refGroup, useInits = NULL, sigOrder = NULL, nIter = 2000, nBurnin = 0, pM1 = 0.5, localTest = TRUE, ... )
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. |
the output jags file
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)