ScoreMatrixBin

BIMSBbioinfo · May 18, 2015 · 8a53824 · 8a53824
1 parent 2fdfebc
commit 8a53824
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Showing 4 changed files with 41 additions and 13 deletions.
diff --git a/R/scoreMatrix.R b/R/scoreMatrix.R
@@ -75,7 +75,7 @@ readBam = function(target, windows, rpm=FALSE,
     }
   }else{
     if(class(param) == 'ScanBamParam'){
-      bamWhich(param) <- reduce(windows, ignore.strand=TRUE) #TODO?
+      bamWhich(param) <- reduce(windows, ignore.strand=TRUE)
     }else{
       stop('param needs to be an object of class ScanBamParam')
     }
@@ -85,7 +85,7 @@ readBam = function(target, windows, rpm=FALSE,
 
     alnpairs <- readGAlignmentPairs(target, param=param, use.names=TRUE)
     # remove duplicate rows
-    #e.g. when every read from pair maps into two different windows, then the pair is duplicated in alnpairs
+    #e.g. when each read from pair maps into two different windows, then the pair is duplicated in alnpairs
     uniq.names.alnpairs <- unique(names(alnpairs))
     ap <- GAlignmentPairs(names=names(alnpairs[1]), first=first(alnpairs[1]), last=last(alnpairs[1]), isProperPair=TRUE)
     for(i in 2:length(uniq.names.alnpairs)){
@@ -355,8 +355,8 @@ setMethod("ScoreMatrix",signature("character","GRanges"),
 
             if(type == 'bam')
               covs = readBam(target, windows, rpm=rpm, unique=unique, 
-                             extend=extend, param=param, paired.end=bam.paired.end,
-                             stranded=stranded)
+                             extend=extend, param=param, 
+                             paired.end=bam.paired.end, stranded=stranded)
             if(type == 'bigWig')
               covs = readBigWig(target=target, windows=windows)            
 

diff --git a/R/scoreMatrixBin.R b/R/scoreMatrixBin.R
@@ -143,7 +143,10 @@ summarizeViewsRle = function(my.vList, windows, bin.op, bin.num, strand.aware){
 #'               based on chr, start, end and strand
 #' @param extend numeric which tells the function to extend the reads to width=extend
 #' @param param ScanBamParam object 
-#'                   
+#' @param bam.paired.end boolean indicating whether given BAM file contains paired-end reads (default:FALSE).
+#'                       Paired-reads will be treated as fragments.
+#' @param stranded boolean which tells whether given BAM file is from a strand-specific protocol (default:TRUE). If FALSE then 
+#'                 strands of reads will be set up to "*".               
 #'                                                 
 #' @return returns a \code{scoreMatrix} object
 #' 
@@ -173,7 +176,9 @@ setGeneric("ScoreMatrixBin",
                     rpm=FALSE,
                     unique=FALSE,
                     extend=0,
-                    param=NULL
+                    param=NULL,
+                    bam.paired.end=FALSE,
+                    stranded=TRUE
                     ) 
              standardGeneric("ScoreMatrixBin") )
 
@@ -246,11 +251,14 @@ setMethod("ScoreMatrixBin",signature("GRanges","GRanges"),
 # ---------------------------------------------------------------------------- #
 #' @aliases ScoreMatrixBin,character,GRanges-method
 #' @rdname ScoreMatrixBin-methods
-#' @usage \\S4method{ScoreMatrixBin}{character,GRanges}(target, windows, bin.num=10, bin.op='mean', strand.aware, type, rpm, unique, extend, param)
+#' @usage \\S4method{ScoreMatrixBin}{character,GRanges}(target, windows, bin.num=10, bin.op='mean', 
+#'                                                      strand.aware, type, rpm, unique, extend, param,
+#'                                                      bam.paired.end=FALSE, stranded=TRUE)
 setMethod("ScoreMatrixBin",signature("character","GRanges"),
           function(target, windows, bin.num=10, 
                    bin.op='mean', strand.aware, 
-                   type, rpm, unique, extend, param){
+                   type, rpm, unique, extend, param,
+                   bam.paired.end=FALSE, stranded=TRUE){
 
             if(!file.exists(target)){
               stop("Indicated 'target' file does not exist\n")
@@ -267,7 +275,8 @@ setMethod("ScoreMatrixBin",signature("character","GRanges"),
 
             if(type == 'bam')
               covs = readBam(target, windows, rpm=rpm, unique=unique, 
-                             extend=extend, param=param)
+                             extend=extend, param=param,
+                             paired.end=bam.paired.end, stranded=stranded)
             if(type == 'bigWig')
               covs = readBigWig(target=target, windows=windows)        
 

diff --git a/inst/unitTests/test_ScoreMatrixBin.R b/inst/unitTests/test_ScoreMatrixBin.R
@@ -100,7 +100,11 @@ test_ScoreMatrixBin_character_GRanges = function()
                    strand=c('-', '-', '-', '-', '+', '-', '+', '-', '-', '-', '-', '-', '-', '+'))
   windows = GRanges(rep(c(1,2),each=2), IRanges(rep(c(1,2), times=2), width=5), 
                     strand=c('-','+','-','+'))
-
+  target.paired.end = GRanges(rep(1,each=7), 
+                              IRanges(c(1,1,2,3,7,8,9), width=c(19, 19, 19, 19, 16, 16, 16)),
+                              strand=rep("+", times=7))
+  windows.paired.end = GRanges(rep(c(1),each=4), IRanges(c(7,8,20, 21), width=10), 
+                               strand=c('+','+','+','+'))
   # -----------------------------------------------#
   # usage
   # bam file
@@ -121,10 +125,16 @@ test_ScoreMatrixBin_character_GRanges = function()
   checkEquals(s3,m3)
 
   #bam file, rpm=FALSE, unique=TRUE, extend=1
-  s4 = ScoreMatrixBin(bam.file, windows, type='bam',bin.num=2, unique=T, extend=1)
+  s4 = ScoreMatrixBin(bam.file, windows, type='bam', bin.num=2, unique=T, extend=1)
   m4 = ScoreMatrixBin(resize(unique(target), width=1), windows, bin.num=2)
   checkEquals(s4,m4)
 
+  # bam file with paired-end reads, rpm=FALSE, unique=TRUE, extend=16
+  bam.pe.file = system.file('unitTests/test_pairedend.bam', package='genomation')
+  s5 = ScoreMatrixBin(bam.pe.file, windows.paired.end, type='bam', bam.paired.end=TRUE, unique=TRUE, extend=16)
+  m5 = ScoreMatrixBin(resize(unique(target.paired.end), width=16), windows.paired.end)
+  checkEquals(s5,m5)
+
   #bigWig file - missing
 
   # -----------------------------------------------#

diff --git a/man/ScoreMatrixBin-methods.Rd b/man/ScoreMatrixBin-methods.Rd
@@ -10,13 +10,16 @@
 \usage{
 ScoreMatrixBin(target, windows, bin.num = 10, bin.op = "mean",
   strand.aware = FALSE, weight.col = NULL, is.noCovNA = FALSE,
-  type = "", rpm = FALSE, unique = FALSE, extend = 0, param = NULL)
+  type = "", rpm = FALSE, unique = FALSE, extend = 0, param = NULL,
+  bam.paired.end = FALSE, stranded = TRUE)
 
 \\S4method{ScoreMatrixBin}{RleList,GRanges}(target, windows, bin.num, bin.op, strand.aware)
 
 \\S4method{ScoreMatrixBin}{GRanges,GRanges}(target,windows,bin.num,bin.op,strand.aware,weight.col,is.noCovNA)
 
-\\S4method{ScoreMatrixBin}{character,GRanges}(target, windows, bin.num=10, bin.op='mean', strand.aware, type, rpm, unique, extend, param)
+\\S4method{ScoreMatrixBin}{character,GRanges}(target, windows, bin.num=10, bin.op='mean',
+                                                     strand.aware, type, rpm, unique, extend, param,
+                                                     bam.paired.end=FALSE, stranded=TRUE)
 }
 \arguments{
 \item{target}{\code{RleList},  \code{GRanges}, BAM file or a bigWig file
@@ -63,6 +66,12 @@ based on chr, start, end and strand}
 \item{extend}{numeric which tells the function to extend the reads to width=extend}
 
 \item{param}{ScanBamParam object}
+
+\item{bam.paired.end}{boolean indicating whether given BAM file contains paired-end reads (default:FALSE).
+Paired-reads will be treated as fragments.}
+
+\item{stranded}{boolean which tells whether given BAM file is from a strand-specific protocol (default:TRUE). If FALSE then
+                strands of reads will be set up to "*".}
 }
 \value{
 returns a \code{scoreMatrix} object