processSNV: Estimate mutation frequency in tri-nucleotide motif contexts.

Description Usage Arguments Details Value See Also Examples

View source: R/processSNV.R

Description

Estimate frequency of point mutations in tri-nucleotide motif contexts for one or more input samples.

Usage

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processSNV(snv, bsg = BSgenome.Hsapiens.UCSC.hg19::Hsapiens)

Arguments

snv

A dataframe having sample, chr, pos, ref, alt and/or freq as its columns. The snv dataframe can be created by the vcfToSNV function.

bsg

An object of class BSGenome. Default: BSgenome.Hsapiens.UCSC.hg19::Hsapiens

Details

Estimation of mutation frequency in pre-determined, user-specified nucleotide motif contexts for input samples. The BSgenome object contains the reference genome information, and should be specified for alternative assembly of human genomes or nonhuman reference genomes. The output returns a data frame containing estimated mutation frequencies in the different genomic contexts, as provided in the contextfreq object, for each input sample.

Value

A data frame of class contextfreq containing mutation frequency in user-specified nucleotide contexts.

See Also

vcfToSNV to generate snv dataframe, BSgenome and BSgenome.Hsapiens.UCSC.hg19.

Examples

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data(snv_sample)
context.freq=processSNV(snv=snv_sample, bsg = BSgenome.Hsapiens.UCSC.hg19::Hsapiens)

sjdlabgroup/MutSigTools documentation built on Oct. 5, 2019, 3:31 a.m.