BayesNMF.MutationalSignatures: Perform Bayesian NMF mutational signature analysis

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

Perform Bayesian NMF mutational signature analysis. Source code borrowed from Broad Institute CGA.

Usage

BayesNMF.MutationalSignatures(x, tumor.type="tumor.type", hyper=FALSE, fafile=NULL, out.dir="OUTPUT_lego96", prior="L1KL")

Arguments

x	A data frame with at least 6 named columns, i.e. 'chr', 'start', 'end', 'ref', 'alt' and 'sampleid'. The seqlevels of mutation data and reference must be identical, or ERROR will occur during mutation context extraction.
tumor.type	A character string specify tumor type analyzed.
hyper	Default = FALSE ; TRUE - to reduce the effect of hyper-mutant samples in the signature discovery.
fafile	BWA-indexed reference sequence. If this is NULL (default), the Homo sapiens hg19 in package BSgenome.Hsapiens.UCSC.hg19 is used. In this case, BSgenome.Hsapiens.UCSC.hg19 must be installed in advanced.
out.dir	The output directory.
prior	Default = L1KL (expoential priors); L2KL (half-normal priors).

See Also

Mutational signature analysis framework in package SomaticSignatures

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.