Question: Detect CNVs in target sample
0
3.9 years ago by
ashkot090
ashkot090 wrote:

Hi all,

Using cn.MOPS for CNV detection and it requires optimally 6 samples (6 BAM files) to effectively run the analysis. I am generating CNV plots for each chromosome but I believe it outlines the CNVs for all samples.

What I want is generate plots for CNVs detected in any one sample i.e. generate CNV plots for every chromosome for any sample. How can that be done?

cn.mops cnv • 801 views
modified 3.9 years ago by Günter Klambauer540 • written 3.9 years ago by ashkot090
Answer: Detect CNVs in target sample
0
3.9 years ago by
Austria
Günter Klambauer540 wrote:

Have you tried segplot(resCNMOPS,...) ? This function should do exactly what you request...

Thanks, this worked, how to save the segplot as an image?

1
pdf("mySegplot.pdf")

segplot(resCNMOPS) # or: segplot(resCNMOPS,toFile=TRUE)

dev.off()

Hi,

if I want to plot all the chromosomes together in one graph, what argument should I set? I can not find it in help. it only says

 plot.type the type of plot. (Default = "s"). what other options?   Thanks!