make_matrix: Converts somatic mutation call files in a directory either in...

Description Usage Arguments Examples

View source: R/make_matrix.R

Description

Converts somatic mutation call files in a directory either in the form of vcf or maf into a 96-dimensional matrix, it works for general number of context and for 1 or 2 strands

Usage

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make_matrix(directory, file_type = "vcf",
  ref_genome = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
  ncontext = 3, nstrand = 1, chrom_colname = NULL,
  pos_colname = NULL, ref_colname = NULL, alt_colname = NULL)

Arguments

directory

pointer to the directory where input vcf maf files reside

file_type

'maf', 'vcf' or 'custom'

ref_genome

name of the BSgenome currently set by default to BSgenome.Hsapiens.UCSC.hg19

ncontext

number of bases in the nucleotide sequence which makes up the spectrum, default 3

nstrand

number of strands to be considered, 1 contracts to a single strand which for ncontext = 3 gives the commonly used 96 dimensions

chrom_colname

used only for custom files a character string defining the colname which holds the chromosome number

pos_colname

used only for custom files a character string defining the colname which holds the position information

ref_colname

used only for custom files a character string defining the colname which holds the ref allele

alt_colname

used only for custom files a character string defining the colname which holds the alt allele

Examples

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by default runs on vcf input and produces 96 dimensional spectra 
make_matrix(directory = 'input')
make_matrix(directory = 'input', 
            file_type = 'vcf',
            ref_genome = BSgenome.Hsapiens.UCSC.hg19,
            ncontext = 5,
            nstrand = 2)

parklab/SigMA documentation built on Oct. 3, 2020, 9:04 a.m.