Incorrect AMP filtering

[arichards2564]

facets-suite/R/gene-level-changes.R

Line 111 in 8a6e371

genes_all[cn_state %like% '^AMP' & length > max_seg_length & (tcn > 8 | genes_on_seg > max_gene_count) , filter := add_tag(filter, 'unfocal_amp')]

This line and the next are incorrect. The filters for cf and number of genes on segment are only being applied when the amp is already too big. These are 3 separate filters and should be applied as such: 1) bp size, 2) cf too low, 3) # genes on segment is too large.
Also, tcn > 8 is good, now bad so I'm not sure why that's being flagged.

I think it needs to be re-written to look like the previous version. This one tries to separate the types of failing CNAs but because we only need 1 of the 3 factors to "PASS" in order to pass the CNA, it doesn't really work.

facets-suite/geneLevel.R

Lines 327 to 338 in 97b1e7e

	genelevelcalls0 = genelevelcalls0 %>%
	mutate(
	# CCS filter flag amplifications and homdels at given thresholds
	ccs_filter = case_when(
	FACETS_CALL.em %in% c("AMP","AMP (LOH)","AMP (BALANCED)") &
	!(seg.len < max_seg_length & (tcn.em > 8 | count <= 10 | ( !is.na(purity) & cf.em > CFcut ))) ~ 'FAIL',
	FACETS_CALL.em == "HOMDEL" & !(seg.len < max_seg_length & count <= 10) ~ 'FAIL',
	TRUE ~ 'PASS'),
	# Flag for review certain homdels
	review = ifelse(ccs_filter == 'FAIL' & FACETS_CALL.em == "HOMDEL" &
	Hugo_Symbol %in% unique(oncokb_tsg$hugoSymbol) & seg.len < 25000000, 'rescue', NA_character_)
	)