Question: Detect CNVs in target sample
0
gravatar for ashkot09
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?

Thanks in advance.

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

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

ADD COMMENTlink written 3.9 years ago by Günter Klambauer540

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

ADD REPLYlink written 3.9 years ago by ashkot090
1
pdf("mySegplot.pdf")

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

dev.off()
ADD REPLYlink written 3.9 years ago by Günter Klambauer540

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!

ADD REPLYlink written 3.0 years ago by tangming2005150
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