Detect CNVs in target sample
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ashkot09 • 0
@ashkot09-9452
Last seen 5.7 years ago

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.

CNV cn.mops • 959 views
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@gunter-klambauer-5426
Last seen 8 months ago
Austria

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

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

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pdf("mySegplot.pdf")

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

dev.off()
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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!

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