adjust_loh              Trim LOH segments with respect to loss
                        segments.
armlevel_alt            Get all globally-altered chromosome arms.
cntypes                 Accepted types of CN for the segments - 'Gain':
                        1-2 extra copies - 'Weak amplification': 3-7
                        extra copies - 'Strong amplification': 8 or
                        more extra copies - 'Heterozygote loss': Loss
                        of one copy out of two - 'Homozygote loss':
                        Loss of all copies - 'LOH': copy-neutral loss
                        of one parental allele
get_amp_segments        Return all segments with an amplification (5 or
                        more copies).
get_gain_segments       Return all segments with gain of copies.
get_hetloss_segments    Return all segments with heterozygous loss.
get_homloss_segments    Return all segments with homozygous loss.
get_loh_segments        Return all segments of type LOH, independently
                        of the copy number.
get_loss_segments       Return all segments with loss of 1 or 2 copies.
get_oncoscan_coverage_from_bed
                        Load the oncoscan coverage BED file into a
                        GenomicRanges object.
load_ascat              Load am ASCAT text export file.
load_chas               Load a ChAS text export file.
merge_segments          Merge segments with respect to the kit
                        resolution and the copy number.
oncoscan_na33.cov       GenomicRanges object of the chromosomal arms
                        coverage for the oncoscan assay (based on file
                        extdata/Oncoscan.na33.r2.cov.processed.bed).
prune_by_size           Remove segments smaller than the kit
                        resolution.
score_avgcn             Compute the average copy number variation
                        across the genome.
score_estwgd            Estimates the number of whole-genome doubling
                        events (WGD).
score_gloh              Compute the genomic LOH score.
score_loh               Compute the number HR deficiency-associated LOH
                        regions.
score_lst               Compute the number of Large-scale State
                        Transitions (LSTs).
score_mbalt             Computes the total number of Mbp altered.
score_nlst              Compute the number of LSTs, normalized by the
                        number of WGD events.
score_td                Compute the number of large tandem duplication
                        (TDplus).
segs.chas_example       Expected segments from loading the ChAS file
                        'chas_example.txt'.
trim_to_coverage        Trim segments with respect to the kit's
                        coverage.
workflow_oncoscan.ascat
                        Run the standard workflow for ASCAT files (from
                        oncoscan data).
workflow_oncoscan.chas
                        Run the standard workflow for Oncoscan ChAS
                        files.
