Kdreval
commented
8 months ago Another issue with this function is:
- in some cases the calculated CCF is nonsensical
- it expects to read from file on disk instead of accepting input data frames
- it is hard-coded to only work with battenberg outputs
- it cannot accept level_3 inputs (more than 1 patient in the merged file)
More details and issues here
It looks like some updates have broken how estimate_purity would obtain the MAF data for a sample. This should be fixed so we can use the augment_ssm output with the auto-removal of variants with low read support.
pure=estimate_purity(sample_id="12-17272_tumorB") fetching: slms-3 using flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--grch37/12-17272_tumorB--12-17272_normal_subclones.igv.seg Rows: 45 Columns: 6 ── Column specification ──────────────────────────────────────────────────────────────────────────────────────── Delimiter: "\t" chr (2): ID, chrom dbl (4): start, end, LOH_flag, log.ratio
ℹ Use spec() to retrieve the full column specification for this data. ℹ Specify the column types or set show_col_types = FALSE to quiet this message. Error in UseMethod("filter") : no applicable method for 'filter' applied to an object of class "NULL"