Generate Human Readable Relative Copy-Number Profiles

This function takes as input a QDNAseq or CGHcall copy-number object and gives back a long-format table with several useful columns. These columns include; 'sample_id', 'chromosome', 'start', 'end', 'gain_probability', 'loss_probability', 'relative_copy_number', 'bin_count', 'sum_of_bin_lengths', 'cytobands', 'coordinates', and 'size'

Usage

GenHumanReadableRcnProfile(object, binsize, ref_genome, save_dir = FALSE)

Arguments

object

S4 copy-number object - QDNAseq or CGHcall object

binsize

The binsize used in the copy number object. ex. '30kb', '100kb'

ref_genome

One of the common reference genomes: ex. 'hg19', 'mm10', or 'hg38'

save_dir

(optional) The directory where the tables should be saved. ex. '~/Documents/test_project'

Value

Segment tables in long format (by sample id) ready to be written out to a table file (ex. tsv, csv).