Hello, I'm using Control FREEC to generate a copy number profile(Normalized copy number) of tumor samples. Although I've generated a profile, I have a doubt. Please see the profile in which red color suggests copy number gain. But I don't know what does each dots represent? Could anyone please describe that? I have used the following commands using R:
getwd() [1] "~/FREEC-11.5/output" ploidy = 2 > ratio <- read.table("Tumor.recal.bam_ratio.txt", header = TRUE) > png(filename = "Tumor_plot.png",width = 1180, height = 1180,units = "px", pointsize = 20, bg = "white", res=NA) > plot(ratio$Start,ratio$Ratioploidy,ylim = c(0,3ploidy),xlab = paste ("Position\n Tumor"),ylab = "Normalised copy number profile", pch = ".", col = "black", cex = 4)
gains <- which(ratio$CopyNumber > ploidy ) > points(ratio$Start[gains], ratio$Ratio[gains]ploidy, pch = ".", col = "blue", cex = 4) > losses <- which(ratio$CopyNumber < ploidy) >points(ratio$Start[losses],ratio$Ratio[losses]ploidy,pch = ".", col = "green", cex = 4)
Please see the left panel of the following figure:
