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?

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!