library(NoWaves)
setwd("C:\\VUData\\CGHdata\\NoWaves")
CGHTumor <- read.table("Dutch_tumor.txt",header=TRUE, sep="\t", na.strings = c("NA","#N/A"),comment.char="%")
#OR load("Dutch_tumor.Rdata") #should contains object called CGHTumor 
load("C:\\VUData\\Normals44K\\Dutch_clingenet.Rdata")
NormalsSmooth <- SmoothNormals(CGHNormal,bandwidth=1)
#save(NormalsSmooth,file="C:\\VUData\\Normals44K\\NormalsSmooth44.Rdata")
load("C:\\VUData\\\\Normals44K\\NormalSmooth44.Rdata")
cormat <- CorTumNorm(CGHTumor,NormalsSmooth)
cormat
corrected <- CorrectTumors(CGHTumor,NormalsSmooth)
plotboth(samp=2,CGHTumor,corrected)
write.table(corrected, file="corrected_tumor.txt", sep="\t", quote=F,row.names=F)
#save(corrected, file="corrected_tumor.Rdata")