getRecurrence: panConusig::getRecurrence

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

panConusig::getRecurrence

Description

Calculates the recurrence of signatures across the genome.

Usage

getRecurrence(sample,chrom,start,end,CNS,
                         windowsGR,sigNames,
                         tumType,
                         ncores=8,returnCounts=FALSE)

Arguments

sample	Vector of sample names for each segment from a set of copy number profiles.
chrom	Vector of chromosome names for each segment from a set of copy number profiles.
start	Vector of start positions for each segment from a set of copy number profiles.
end	Vector of end positions for each segment from a set of copy number profiles.
CNS	Vector of signature assignments for each segment from a set of copy number profiles. See runAssignment() for method to assign copy number signatures to segments.
windowsGR	GenomicRanges object with windows in which to evaluate recurrence of signatures. Can be generated using setupWindows().
sigNames	Vector if signature names for which to evaluate recurrence. Should match those in CNS.
ncores	Number of cores to use for calculation. Defaults to 8.
returnCounts	Boolean. Whether to return counts of recurrence (TRUE), or proportions (FALSE).

Value

A matrix giving the proportion or count of samples with a signature recurrence in a given genomic window. Matrix will be of wxn where w is the number of genomic windows and n is the number if signatures listed in sigNames.

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