setupWindows: panConusig::setupWindows

In UCL-Research-Department-of-Pathology/panConusig: Pan-cancer copy number signatures analysis

panConusig::setupWindows

Description

Split the genome into windows of a given size (windowLength). Used as input when calculating recurrence of signatures across the genome.

Usage

setupWindows(chr,startpos,endpos,
windowLength = 1000000,doBiomart=FALSE)

Arguments

chr	Vector of chromesome labels for all segments from all copy numebr profiles.
startpos	Vector of start positions for all segments from all copy numebr profiles.
endpos	Vector of end positions for all segments from all copy numebr profiles.
windowLength	Length of genomic windows to be returned, in bases.
doBiomart	Boolean. Whether to return a biomart mart object. Used when plotting gene names in plotRecurrence(), if a gene genomicRanges object is not supplied.

Value

List of: [[windows]]=matrix of genomic windows, [[windowsGR]]=GenomicRanges object of genomic windows, [[splits]]=genomic windows that denote boundaries between chromosomes, [[mids]]=genomic windows that denot midpoints of chromosomes, [[ensembl]]=biomart mart object.

UCL-Research-Department-of-Pathology/panConusig documentation built on March 25, 2022, 12:18 a.m.