From 63f464bc2096c1d77a660aba92636194a5eee81a Mon Sep 17 00:00:00 2001 From: Stef Piatek Date: Tue, 4 Jun 2019 10:44:10 +0100 Subject: [PATCH] group panelcn.mops calls --- .../panelcn_mops/panelcn_mops_runner.R | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/cnv-caller-resources/panelcn_mops/panelcn_mops_runner.R b/cnv-caller-resources/panelcn_mops/panelcn_mops_runner.R index 63f414c..2eee58c 100755 --- a/cnv-caller-resources/panelcn_mops/panelcn_mops_runner.R +++ b/cnv-caller-resources/panelcn_mops/panelcn_mops_runner.R @@ -28,6 +28,16 @@ detect_cnvs <- function(sample_number) { cnv_results <- raw_results[[1]] %>% filter(CN != "CN2") %>% mutate(Sample = unknown_samples$sample_name[sample_number]) %>% + group_by(Sample, Chr, Gene, CN) %>% + summarise(Exon = paste(min(as.character(Exon)), max(as.character(Exon))), + Start = min(Start, End), + End = max(Start, End), + RC = mean(RC), + medRC = mean(medRC), + `RC.norm` = mean(`RC.norm`), + `medRC.norm` = mean(`medRC.norm`), + lowQual = min(as.character(lowQual)) + ) %>% return() } @@ -56,7 +66,8 @@ normals <- countBamListInGRanges(countWindows = count_windows, bam.files = norma unknowns <- countBamListInGRanges(countWindows = count_windows, bam.files = unknown_samples$bam_path, read.width = 150) # Run CNV calling -called_cnvs <- map_dfr(.x = seq(1, nrow(unknown_samples)), .f = detect_cnvs) +called_cnvs <- map_dfr(.x = seq(1, nrow(unknown_samples)), .f = detect_cnvs) %>% + filter(!is.na(Sample)) # Save results write.table(called_cnvs, file = file.path(opt$output_path, "calls.tsv"), sep = "\t", quote = FALSE, row.names = FALSE)