Question: Copy number profile using Control-FREEC
gravatar for tanbiswas6
12 months ago by
tanbiswas60 wrote:

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:

ADD COMMENTlink modified 12 months ago by Kevin Blighe67k • written 12 months ago by tanbiswas60
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

As you have used _ratio.txt, each dot represents the predicted copy number for each window.

The size of the window will depend on your input configuration file.


ADD COMMENTlink written 12 months ago by Kevin Blighe67k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1957 users visited in the last hour