Package: oncoscanR 1.9.0

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]

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oncoscanR.pdf |oncoscanR.html✨
oncoscanR/json (API)
NEWS

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

Peer review:

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-1.7.2(bioc 3.20)oncoscanR-1.6.0(bioc 3.19)

copynumbervariationmicroarraysoftware

4.60 score 2 stars 6 scripts 146 downloads 24 exports 41 dependencies

Last updated 23 days agofrom:bef9380f70. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:adjust_loharmlevel_altget_amp_segmentsget_gain_segmentsget_hetloss_segmentsget_homloss_segmentsget_loh_segmentsget_loss_segmentsget_oncoscan_coverage_from_bedload_ascatload_chasmerge_segmentsprune_by_sizescore_avgcnscore_estwgdscore_glohscore_lohscore_lstscore_mbaltscore_nlstscore_tdtrim_to_coverageworkflow_oncoscan.ascatworkflow_oncoscan.chas

Dependencies:askpassBiocGenericsbitbit64clicliprcpp11crayoncurlfansiGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehmshttrIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogressR6readrrlangS4VectorssystibbletidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXVectorzlibbioc

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

Yann Christinat

Rendered fromoncoscanR.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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 allelecntypes
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