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

In parklab/SigMA: Signature Multivariate Analysis

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

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

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

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 Aug. 11, 2024, 8:49 p.m.