fix error which caused errors with 0% altered arms in WGS samples

Liam Flinn Spurr · Liam Flinn Spurr · commit b499f5c6349d · 2024-01-24T14:49:54.000-06:00
diff --git a/ascets_resources.R b/ascets_resources.R
@@ -260,7 +260,8 @@ compute_alt_fractions <- function(cna, amp_thresh, del_thresh, min_boc) {
     ungroup() %>%
     mutate(alt_frac = alt_len_sum / cyto_len_corr) %>%  # calculate the fraction
     dplyr::select(sample, arm, alt, perc_chrom_cov, cov_pass, alt_frac) %>%
-    distinct()
+    distinct() %>%
+    mutate(alt_frac = ifelse(is.na(alt_frac), 0, alt_frac))
 }
 
 calc_aneu_scores <- function(calls) {

Original file line number	Diff line number	Diff line change
`@@ -260,7 +260,8 @@ compute_alt_fractions <- function(cna, amp_thresh, del_thresh, min_boc) {`
`260`	`260`	`ungroup() %>%`
`261`	`261`	`mutate(alt_frac = alt_len_sum / cyto_len_corr) %>% # calculate the fraction`
`262`	`262`	`dplyr::select(sample, arm, alt, perc_chrom_cov, cov_pass, alt_frac) %>%`
`263`		`- distinct()`
	`263`	`+ distinct() %>%`
	`264`	`+ mutate(alt_frac = ifelse(is.na(alt_frac), 0, alt_frac))`
`264`	`265`	`}`
`265`	`266`
`266`	`267`	`calc_aneu_scores <- function(calls) {`