Package: oncoscanR 1.15.0

Yann Christinat

oncoscanR: Secondary analyses of CNV data (HRD and more)

The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.

Authors:Yann Christinat [aut, cre], Geneva University Hospitals [aut, cph]

oncoscanR_1.15.0.tar.gz
oncoscanR_1.15.0.zip(r-4.7)oncoscanR_1.15.0.zip(r-4.6)oncoscanR_1.15.0.zip(r-4.5)
oncoscanR_1.15.0.tgz(r-4.6-any)oncoscanR_1.15.0.tgz(r-4.5-any)
oncoscanR_1.15.0.tar.gz(r-4.7-any)oncoscanR_1.15.0.tar.gz(r-4.6-any)
oncoscanR_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
oncoscanR/json (API)

# Install 'oncoscanR' in R:

install.packages('oncoscanR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yannchristinat/oncoscanr/issues

Datasets:

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
oncoscan_na33.cov - GenomicRanges object of the chromosomal arms coverage for the oncoscan assay (based on file extdata/Oncoscan.na33.r2.cov.processed.bed).
segs.chas_example - Expected segments from loading the ChAS file 'chas_example.txt'.

On BioConductor:oncoscanR-1.15.0(bioc 3.24)oncoscanR-1.14.0(bioc 3.23)

copynumbervariation microarray software

4.48 score 3 stars 7 scripts 24 exports 30 dependencies

Last updated from:74407d7cd8. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	213
linux-devel-x86_64	OK	406
source / vignettes	OK	279
linux-release-x86_64	OK	349
macos-release-arm64	OK	212
macos-oldrel-arm64	OK	180
windows-devel	OK	336
windows-release	OK	298
windows-oldrel	OK	317
wasm-release	OK	129

Exports:adjust_loh armlevel_alt get_amp_segments get_gain_segments get_hetloss_segments get_homloss_segments get_loh_segments get_loss_segments get_oncoscan_coverage_from_bed load_ascat load_chas merge_segments prune_by_size score_avgcn score_estwgd score_gloh score_loh score_lst score_mbalt score_nlst score_td trim_to_coverage workflow_oncoscan.ascat workflow_oncoscan.chas

Dependencies:BiocGenerics bit bit64 cli clipr cpp11 crayon generics GenomicRanges glue hms IRanges lifecycle magrittr pillar pkgconfig prettyunits progress R6 readr rlang S4Vectors Seqinfo tibble tidyselect tzdb utf8 vctrs vroom withr

Secondary analyses of CNV data (HRD and more) with oncoscanR

Rendered fromoncoscanR.Rmdusingknitr::rmarkdown

Last update: 2023-04-26
Started: 2022-04-19

Citation

Development and contributors

Readme and manuals

Help Manual

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