readBGFile: Read and format the background vector data

In friend1ws/pmsignature: Extracting characteristic mutation signatures from a set of mutation data.

Description

This function provides a background probability for each mutation feature, that is available only when the model type is "independent" or "full", and the numBases is either of 3, 5, 7 or 9.

The background probability vectors are calculated by the function getBackgroudSignature, checking the frequencies of consecutive nucleotides on exonic regions. Therefore, when you are using whole genome sequencing data, using the background signatures provided by this function may not be appropriate.

Usage

readBGFile(mutationFeatureData)

Arguments

mutationFeatureData

the mutation data processed in the function (readMPFile or readMFVFile)

Value

The output is a background probability vector corresponding to the input mutation data.

Examples

inputFile <- system.file("extdata/Nik_Zainal_2012.mutationPositionFormat.txt.gz", package="pmsignature")
G <- readMPFile(inputFile, numBases = 7)
BG_prob <- readBGFile(G)

friend1ws/pmsignature documentation built on May 16, 2019, 3:27 p.m.