Added centomere positions.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@119121 bc3139a8-67e5-0310-9ffc-ced21a209358

R/runAbsoluteCN.R

@@ -35,6 +35,9 @@ vcf.file=NULL,
 ### Again, do not expect very useful results without a VCF file.
 genome,
 ### Genome version, required for the readVcf function.
+centromeres=NULL,
+### Data.frame with centromere positions in first three columns. 
+### If NULL, use pre-stored positions for genome versions hg18, hg19 and hg38. 
 sex=c("?","F","M","diploid"),
 ### Sex of sample. If ?, detect using getSexFromCoverage function and default
 ### parameters. 
@@ -164,6 +167,14 @@ post.optimize=FALSE,
         message("Default of genome=hg19 is deprecated. Please specify genome.")
     }    
 
+    if (is.null(centromeres)) {
+        data(centromeres, envir = environment())
+        if (genome %in% names(centromeres)) {
+            centromeres <- centromeres[[genome]]
+        } else {
+            centromeres <- NULL
+        }
+    }
     # argument checking
     .checkParameters(test.purity, min.ploidy, max.ploidy, max.non.clonal)
 
@@ -811,8 +822,10 @@ post.optimize=FALSE,
             log.ratio.sdev=sd.seg, 
             vcf=vcf, 
             sampleid=sampleid, 
-            sex=sex, sex.vcf=sex.vcf,
-            chr.hash=chr.hash) 
+            sex=sex, 
+            sex.vcf=sex.vcf,
+            chr.hash=chr.hash,
+            centromeres=centromeres) 
         )
 ##end<<
 },ex=function(){

inst/extdata/downloadCentromeres.R

@@ -0,0 +1,31 @@
+library(rtracklayer)
+library(data.table)
+library(PureCN)
+
+data(chr.hash)
+mySession <- browserSession("UCSC")
+genomes <- c("hg18", "hg19", "hg38")
+centromeres <- list()
+
+for (genome in genomes) {
+    genome(mySession) <- genome
+    if (genome == "hg38") {
+        tbl.gaps <- getTable( ucscTableQuery(mySession,track="Centromeres",
+table="centromeres"))
+    } else {
+        tbl.gaps <- getTable( ucscTableQuery(mySession,  track="Gap",
+            table="gap"))
+        tbl.gaps <- tbl.gaps[tbl.gaps$type=="centromere",]
+    }
+    tbl.gaps.dt <- data.table(tbl.gaps)
+    tbl.centromeres <- as.data.frame(tbl.gaps.dt[,
+        list(chromStart=min(chromStart),chromEnd=max(chromEnd)),by=chrom])
+    centromeres[[genome]] <- tbl.centromeres 
+}
+
+centromeres <- lapply(centromeres, function(x) {
+    x$chromNumerical <- chr.hash$number[match(x$chrom, chr.hash$chr)]
+    x[order(x$chromNumerical),1:3]
+})
+
+save(centromeres, file="data/centromeres.rda", compress="xz")

man/centromeres.Rd

@@ -0,0 +1,28 @@
+\name{centromeres}
+\alias{centromeres}
+\docType{data}
+\title{
+A list of data.frames containing centromere positions.
+}
+\description{
+A list of data.frames containing centromere positions for hg18, hg19 and hg38.
+Downloaded from the UCSC genome browser.
+}
+\usage{data(centromeres)}
+\value{
+    A list with three data frames, "hg18", "hg19", and "hg38". Each containes
+three columns
+    \describe{
+        \item{\code{chrom}}{a factor with levels \code{chr1} \code{chr10} \code{chr11} \code{chr12} \code{chr13} \code{chr14} \code{chr15} \code{chr16} \code{chr17} \code{chr18} \code{chr19} \code{chr2} \code{chr20} \code{chr21} \code{chr22} \code{chr3} \code{chr4} \code{chr5} \code{chr6} \code{chr7} \code{chr8} \code{chr9} \code{chrX} \code{chrY}}
+        \item{\code{chromStart}}{a numeric vector}
+        \item{\code{chromEnd}}{a numeric vector}
+    }
+}
+\references{
+The script downloadCentromeres.R in the extdata directory was used to generate
+the data.frames.
+}
+\examples{
+data(centromeres)
+}
+\keyword{datasets}

man/runAbsoluteCN.Rd

@@ -11,8 +11,8 @@ Returns purity and ploidy combinations, sorted by likelihood score.
 Provides copy number and LOH data, by both gene and genomic region. }
 \usage{runAbsoluteCN(gatk.normal.file = NULL, gatk.tumor.file, 
     log.ratio = NULL, seg.file = NULL, seg.file.sdev = 0.4, 
-    vcf.file = NULL, genome, sex = c("?", "F", "M", 
-        "diploid"), fun.filterVcf = filterVcfMuTect, 
+    vcf.file = NULL, genome, centromeres = NULL, sex = c("?", 
+        "F", "M", "diploid"), fun.filterVcf = filterVcfMuTect, 
     args.filterVcf = list(), fun.setPriorVcf = setPriorVcf, 
     args.setPriorVcf = list(), fun.segmentation = segmentationCBS, 
     args.segmentation = list(), fun.focal = findFocal, 
@@ -48,6 +48,8 @@ flag for dbSNP membership. The default fun.setPriorVcf function will also
 look for a Cosmic.CNT slot, containing the hits in the COSMIC database.
 Again, do not expect very useful results without a VCF file.}
   \item{genome}{Genome version, required for the readVcf function.}
+  \item{centromeres}{Data.frame with centromere positions in first three columns. 
+If NULL, use pre-stored positions for genome versions hg18, hg19 and hg38. }
   \item{sex}{Sex of sample. If ?, detect using getSexFromCoverage function and default
 parameters. 
 Default parameters might not work well with every assay and