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

https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=3268243_btr670f1.jpg

ADD COMMENTlink modified 12 months ago by Kevin Blighe67k • written 12 months ago by tanbiswas60
0
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.

Kevin

ADD COMMENTlink written 12 months ago by Kevin Blighe67k
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