Assign copy number calls — annotate_copy

annotate_copy_number returns the data.table dt_sample annotated with allele-specific copy numbers

annotate_copy_number(dt_sample, seg, rm_sex_chrom = FALSE)

Arguments

dt_sample: data.table object with each CpG and their coverage, counts methylated and methylation rate
seg: ASCAT.m copy number segements object
rm_sex_chrom: Logical indicating if you would like to remove sex chrom from downstream analyses

A dataframe for each sample_id with the copy number calls added