Merge pull request #10 from Crick-CancerGenomics/dev

Dev

ASCAT/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ASCAT
 Type: Package
 Title: Allele-Specific Copy Number Analysis of Tumours
-Version: 2.4.3
-Date: 2016-06-20
+Version: 2.4.4
+Date: 2017-04-06
 Authors@R: c(person("Peter", "Van Loo", role=c("aut","cre"), email="[email protected]"),
     person("Gro", "Nielsen", role="ctb"),
     person("Jiqiu","Cheng", role="ctb"),

ASCAT/NAMESPACE

@@ -15,10 +15,7 @@ export(base.gw.plot)
 export(make_segments)
 export(runASCAT)
 import(RColorBrewer)
-importFrom("grDevices", "adjustcolor", "colorRampPalette", "dev.new",
-             "dev.off", "pdf", "png")
-importFrom("graphics", "abline", "axis", "image", "par", "plot",
-             "points", "rect", "text")
-importFrom("stats", "complete.cases", "cor", "lm", "mad", "median",
-             "na.omit", "runmed", "var")
+importFrom("grDevices", "adjustcolor", "colorRampPalette", "dev.new","dev.off", "pdf", "png")
+importFrom("graphics", "abline", "axis", "image", "par", "plot","points", "rect", "text")
+importFrom("stats", "complete.cases", "cor", "lm", "mad", "median","na.omit", "runmed", "var")
 importFrom("utils", "read.table", "write.table")

ASCAT/R/ascat.R

@@ -1,4 +1,4 @@
-# ASCAT 2.4.3
+# ASCAT 2.4.4
 # author: Peter Van Loo
 # PCF and ASPCF: Gro Nilsen
 # GC correction: Jiqiu Cheng
@@ -2155,6 +2155,7 @@ psi <- function(x,z){
 #' HumanCore12\cr
 #' HumanCoreExome24\cr
 #' HumanOmniExpress12\cr
+#' IlluminaOmniExpressExome\cr
 #'
 #' @return predicted germline genotypes
 #'
@@ -2267,18 +2268,28 @@ ascat.predictGermlineGenotypes = function(ASCATobj, platform = "AffySNP6") {
     segmentLength = 100
   }
   else if (platform=="AffyOncoScan") {
-    maxHomozygous = 0.05
-    proportionHetero = 0.24
-    proportionHomo = 0.69
-    proportionOpen = 0.04
+    maxHomozygous = 0.04
+    proportionHetero = 0.355
+    proportionHomo = 0.605
+    proportionOpen = 0.025
     segmentLength = 30
+    # maxHomozygous = 0.05
+    # proportionHetero = 0.24
+    # proportionHomo = 0.69
+    # proportionOpen = 0.04
+    # segmentLength = 30
   }
   else if (platform=="AffyCytoScanHD") {
-    maxHomozygous = 0.05
-    proportionHetero = 0.26
-    proportionHomo = 0.69
+    # maxHomozygous = 0.05
+    # proportionHetero = 0.26
+    # proportionHomo = 0.69
+    # proportionOpen = 0.03
+    # segmentLength = 30
+    maxHomozygous = 0.04
+    proportionHetero = 0.32
+    proportionHomo = 0.60
     proportionOpen = 0.03
-    segmentLength = 30
+    segmentLength = 100
   }
   else if (platform=="HumanCNV370quad") {
     maxHomozygous = 0.05
@@ -2308,6 +2319,13 @@ ascat.predictGermlineGenotypes = function(ASCATobj, platform = "AffySNP6") {
     proportionOpen = 0.015
     segmentLength = 100
   }
+  else if (platform=="IlluminaOmniExpressExome") {
+    maxHomozygous = 0.05
+    proportionHetero = 0.35
+    proportionHomo = 0.60
+    proportionOpen = 0.03
+    segmentLength = 100
+  }
   #   else if (platform=="OmniZhonghua8") {
   #     maxHomozygous = 0.05
   #     proportionHetero = 0.295

gcProcessing/createGCcontentFile.R

@@ -1,14 +1,16 @@
 args <- commandArgs(TRUE)
 
+library(plyr)
+
 data<-read.table(args[1])
 name<-args[2]
 
-agg<-aggregate(data$V8,by=list(data$V4,gsub("chr","", data$V1),data$V5), FUN=t)
-agg<-as.data.frame(as.matrix(agg))
+agg<-ddply(data, .(V4, V1, V5), function(z) return(t(z$V8)))
+cols<-ifelse(unique(data$V6)/1000000>=1, paste(unique(data$V6)/1000000, "M", sep=""), unique(data$V6))
+
 rownames(agg)<-agg[,1]
 agg[,1]<-NULL
 
-cols<-ifelse(unique(data$V6)/1000000>=1, paste(unique(data$V6)/1000000, "M", sep=""), unique(data$V6))
 colnames(agg)<-c("Chr","Position",cols)
 agg<-agg[order(agg$Chr, as.numeric(as.character(agg$Position))),]
 write.table(agg,paste(name,".txt",sep=""),quote=F, row.names=T, sep="\t")