Class CopyNumber

S4 class for storing summarized absolute copy number profile.

Slots

data

data.table of absolute copy number calling.

summary.per.sample

data.table of copy number variation summary per sample.

genome_build

genome build version, should be one of 'hg19' or 'hg38'.

genome_measure

Set 'called' will use autosomo called segments size to compute total size for CNA burden calculation, this option is useful for WES and target sequencing. Set 'wg' will autosome size from genome build, this option is useful for WGS, SNP etc..

annotation

data.table of annotation for copy number segments.

dropoff.segs

data.table of copy number segments dropped from raw input.