NEWS.md
In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)

Versions on bioconductor and Github have been merged and, from now on, will have consistent version numbers.

Added two functions to handle ASCAT files instead of ChAS load_ascat and workflow_oncoscan.ascat.
Main workflow function workflow_oncoscan.run is renamed workflow_oncoscan.chas for consistency with the ASCAT function
Bug fixes in adjust_loh (crashed with segments of length 1 or if no LOH segments where present)
Bug fix in script run_oncoscan_workflow.R

To simplify the workflow, the gender of the patient is not taken into account anymore. That implies that in a male sample, a gain of 3 extra copies on the X or Y chromosome is considered as a gain and not an amplification anymore. For female samples, nothing changes.
The oncoscan coverage has been corrected to reflect only areas where there are groups of probes. Isolated probes where causing issues to identify arm-level alterations as ChAS segments where never extended to these probes and the 90% threshold could never be met (particularly on chromosomal arms 9p and Yq).
Minor corrections in vignette

The nLST test has been clinically validated on 384 patients from the PAOLA-1 trial and the recommended threshold is now >=15.
The default value for arm-level alterations has been set to 90% as mentioned in the publication [Christinat et al., J Mol Diagn 2021; PMID: 34454110].
The genomic LOH score (percent of LOH bases) has been added; score_gloh.
Adds a flag "no tumor?" if the percentage of altered bases is less than 1%.
Package to be released on Bioconductor

Novel HRD score (nLST: number of LSTs, normalized by ploidy): score_nlst
Change in Oncoscan workflow to use the nLST score and thresholds.
New function to compute the number of Mb altered (with or without LOH): score_mbalt
New function to compute the average copy number: score_avgcn
New function to estimate the number of whole-genome duplication events (based on the average copy number and the thresholds defined by Carter et al.): score_estwgd