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Unverified Commit df87f670 authored by Laurent Modolo's avatar Laurent Modolo
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intersect_SNP.R: sort results by AF

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src/intersect_SNP.R
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...@@ -17,7 +17,7 @@ snp <- snp_b %>% ...@@ -17,7 +17,7 @@ snp <- snp_b %>%
filter(cords %in% only_b) filter(cords %in% only_b)
fastafile <- read.fasta(file = args[3], fastafile <- read.fasta(file = args[3],
as.string = TRUE) as.string = TRUE)
snp$seq_list <- snp %>% snp$seq_list <- snp %>%
apply(1, FUN = function(x, fastafile, POS, CHROM){ apply(1, FUN = function(x, fastafile, POS, CHROM){
...@@ -38,5 +38,6 @@ snp$seq_list <- snp %>% ...@@ -38,5 +38,6 @@ snp$seq_list <- snp %>%
) )
snp %>% snp %>%
arrange(desc(tumor_sample.AF)) %>%
write_csv(paste0("only_", args[2])) write_csv(paste0("only_", args[2]))
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