# Secondary analyses of CNV data (HRD and more)

## Documentation for package ‘oncoscanR’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.