Complete with zero alt frequency including region

Author: ahmig

workflow/scripts/report/snp_plots.R

@@ -52,7 +52,7 @@ vcf <- vcf %>%
 
 # Fill positions without alt frequency with 0
 vcf <- vcf %>%
-  complete(nesting(VARIANT_NAME, POS), SAMPLE, fill = list(ALT_FREQ = 0))
+  complete(nesting(REGION, VARIANT_NAME, POS), SAMPLE, fill = list(ALT_FREQ = 0))
 
 # Join variants file and metadata file
 vcf <- left_join(vcf, data, by = c("SAMPLE" = "ID"))
@@ -87,6 +87,7 @@ cor.df <- data.frame(
 cor.df.fill <- lapply(
   SNPs,
   function(snp) {
+    message(snp)
     df <- filter(
       vcf,
       VARIANT_NAME == snp