From d1a3fd5c615fa158a09fb88b2a48bd7c288b5e06 Mon Sep 17 00:00:00 2001
From: wayneliuq <63512373+wayneliuq@users.noreply.github.com>
Date: Tue, 23 Feb 2021 12:24:38 -0500
Subject: [PATCH] correctReadDepth targetedSequence fix

fix bug in correctReadDepth function
---
 R/utils.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils.R b/R/utils.R
index f2be2eb..f5a04fe 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -529,7 +529,7 @@ correctReadDepth <- function(tumWig, normWig, gcWig, mapWig,
     message("Analyzing targeted regions...")
     targetIR <- GRanges(ranges = IRanges(start = targetedSequence[, 2], 
                 end = targetedSequence[, 3]), seqnames = targetedSequence[, 1])
-    names(targetIR) <- setGenomeStyle(names(targetIR), genomeStyle)
+    names(targetIR) <- setGenomeStyle(seqnames(targetIR), genomeStyle)
     hits <- findOverlaps(query = tumour_reads, subject = targetIR)
     keepInd <- unique(queryHits(hits))    
     tumour_reads <- tumour_reads[keepInd, ]