Question: Help With The Dnacopy Number Package In R
gravatar for ivivek_ngs
6.8 years ago by
Seattle,WA, USA
ivivek_ngs5.0k wrote:

Dear All,

I am using the Varscan 2 for my experiments to understand the variants and mutational profile in my tumor an IPS(induced pluripotent stem cells). I am doing the CNA calling using the pakcage DNACopy and using CBS for segmentation. I am trying to understand for each of my test sample(tumor or IPS) at individual chr level how does the profile looks like after plotting, if I can see any amplification or deletion at any chr and if the same thing corresponds to its IPS which is derived from a single clone from the tumor. To this when I use the R code , I see for my tumor and IPS the plot scales are different on the y- axis. I would like to have same scale for both tumor and IPS data. Can anyone suggest me how to do that? I am more interested in controlling the scale Y axis (log2ratio values of mean). I want a scale between -2 to 2 , but I see the scale between -4 to 4 in tumor and for two IPS it is -2 to 2 and-6 to 6. I want to have same scale for all the 3. first I want to have the scale between -2 to 2 and then play with the scale more to see the distinct pattern of the amplifications and deletions at each chr level for the genomic segments. I am attaching the piece of code I used. Any suggestions on changing the scale is welcome.

cn <- read.table("Desktop//CNA/N1vsLG_CNV_filtered.txt",header=T)
CNA.object <-CNA( genomdat = cn[,7], chrom = cn[,1], maploc = cn[,2], data.type = 'logratio',sampleid = "N1vsLG_CNV") ## cn[,5]`
CNA.smoothed <- smooth.CNA(CNA.object)
segs <- segment(CNA.smoothed, verbose=0, min.width=2)
segs2 = segs$output
pdf(file = "~/Desktop/tmp.pdf")
plot(segs, plot.type = "c")

Which should be the parameter I should use to obtain the similar scale for all different comparisons. Please advice.


exome-sequencing • 3.7k views
ADD COMMENTlink modified 6.8 years ago by Sean Davis26k • written 6.8 years ago by ivivek_ngs5.0k

Try plot(...., ylim=c(-2,2)).

ADD REPLYlink written 6.8 years ago by Sean Davis26k

Yes thanks now it is working, I was taking the scale wrong

ADD REPLYlink written 6.8 years ago by ivivek_ngs5.0k

If each of your tumors can be matched with an IPS sample, isnt it better to calculate the log2(tumor/IPS) and use that as input for DNAcopy ?

ADD REPLYlink written 6.8 years ago by Irsan7.2k

They are actually log2 values only as far as I know. The VarScan uses the log2 values only for CNV analysis and then uses CBS with the DNAcopy tool.

ADD REPLYlink written 6.8 years ago by ivivek_ngs5.0k
gravatar for Sean Davis
6.8 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

Just echoing my comment since it seemed to do the trick.

plot(...., ylim=c(-2,2))
ADD COMMENTlink written 6.8 years ago by Sean Davis26k
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: 2154 users visited in the last hour