Secondary analyses of CNV data (HRD and more)

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Documentation for package ‘oncoscanR’ version 1.11.1

• 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.