Man pages for yannchristinat/oncoscanR
Secondary analyses of CNV data (HRD and more)
| 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... |
| 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... |
| 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... |
| 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... |
| oncoscan_na33.cov | GenomicRanges object of the chromosomal arms coverage for the... |
| oncoscanR-package | oncoscanR: an R package to perform secondary analysis of Copy... |
| 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... |
| score_td | Compute the number of large tandem duplication (TDplus). |
| segs.chas_example | Expected segments from loading the ChAS file... |
| trim_to_coverage | Trim segments with respect to the kit's coverage. |
| workflow_oncoscan.ascat | Run the standard workflow for ASCAT files (from oncoscan... |
| workflow_oncoscan.chas | Run the standard workflow for Oncoscan ChAS files. |
