Question

Detect CNVs in target sample

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ashkot09 • 0

@ashkot09-9452

Last seen 8.9 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 • 1.8k views

ADD COMMENT • link updated 8.9 years ago by Günter Klambauer ▴ 540 • written 8.9 years ago by ashkot09 • 0

score 0 · Answer 1 · 2016-01-13

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Günter Klambauer ▴ 540

@gunter-klambauer-5426

Last seen 3.8 years ago

Austria

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

ADD COMMENT • link 8.9 years ago Günter Klambauer ▴ 540

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

ADD REPLY • link 8.9 years ago ashkot09 • 0

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pdf("mySegplot.pdf")

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

dev.off()

ADD REPLY • link 8.9 years ago Günter Klambauer ▴ 540

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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!

ADD REPLY • link 8.0 years ago tangming2005 ▴ 200