From b028236e089a448b60db4b4a92af975b2d08abc6 Mon Sep 17 00:00:00 2001
From: "a.deschenes" <a.deschenes@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: Thu, 31 Dec 2015 02:57:08 +0000
Subject: [PATCH 1/2] Update importFrom section for findConsensusPeakRegions()
 function

From: adeschen <adeschen@hotmail.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/consensusSeekeR@112057 bc3139a8-67e5-0310-9ffc-ced21a209358
---
 NAMESPACE                    | 1 +
 R/findConsensusPeakRegions.R | 8 ++++----
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index a2a03ee..1e3506a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,5 +12,6 @@ importFrom(BiocParallel,SnowParam)
 importFrom(BiocParallel,bplapply)
 importFrom(BiocParallel,bpmapply)
 importFrom(BiocParallel,multicoreWorkers)
+importFrom(GenomicRanges,split)
 importFrom(rtracklayer,import)
 importFrom(stringr,str_split)
diff --git a/R/findConsensusPeakRegions.R b/R/findConsensusPeakRegions.R
index 490849d..f0a69df 100644
--- a/R/findConsensusPeakRegions.R
+++ b/R/findConsensusPeakRegions.R
@@ -127,6 +127,7 @@
 #' ## Print 2 first consensus regions
 #' head(results$consensusRanges, 2)
 #'
+#' @importFrom GenomicRanges split
 #' @export
 findConsensusPeakRegions <- function(narrowPeaks, peaks, chrInfo,
                                 extendingSize = 250,
@@ -157,7 +158,7 @@ findConsensusPeakRegions <- function(narrowPeaks, peaks, chrInfo,
     areNarrowPeaksUsed <- expandToFitPeakRegion | shrinkToFitPeakRegion
 
     # Preparing peak data
-    peaksSplit <- GenomicRanges::split(peaks, seqnames(peaks))
+    peaksSplit <- split(peaks, seqnames(peaks))
     rm(peaks)
 
     selectedPeaksSplit <- peaksSplit[names(peaksSplit) %in%
@@ -166,8 +167,7 @@ findConsensusPeakRegions <- function(narrowPeaks, peaks, chrInfo,
 
     # Preparing narrow peaks data
     if (areNarrowPeaksUsed) {
-        narrowPeaksSplit <- GenomicRanges::split(narrowPeaks,
-                                                    seqnames(narrowPeaks))
+        narrowPeaksSplit <- split(narrowPeaks, seqnames(narrowPeaks))
         rm(narrowPeaks)
 
         selectedNarrowPeaksSplit <- narrowPeaksSplit[names(narrowPeaksSplit)
@@ -191,7 +191,7 @@ findConsensusPeakRegions <- function(narrowPeaks, peaks, chrInfo,
 
     # Creating result list
     z <- list(call = cl,
-                consensusRanges = IRanges::unlist(GRangesList((results)),
+                consensusRanges = unlist(GRangesList((results)),
                 recursive = TRUE,
                 use.names = FALSE))
 

From fbb2c85786b308b5d9bc62abdd85ee4c5b2ae427 Mon Sep 17 00:00:00 2001
From: "a.deschenes" <a.deschenes@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: Thu, 31 Dec 2015 02:57:20 +0000
Subject: [PATCH 2/2] Update package version to 0.99.6

From: adeschen <adeschen@hotmail.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/consensusSeekeR@112058 bc3139a8-67e5-0310-9ffc-ced21a209358
---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4f79de9..5bf75b0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: consensusSeekeR
-Version: 0.99.5
+Version: 0.99.6
 Date: 2015-05-01
 Title: Detection of consensus regions inside a group of experiences using
     genomic positions and genomic ranges