How to plot datasets from VarScan2 in R.

pablosantamarta · 03-22-2012, 02:37 AM

Hi everybody,

I'm using VarScan2's Somatic Mutation Calling function and the output are two files with a large number of columns. I wanna represent graphically two columns (normal_var_freq(column 7) and tumor_var_freq(column 11)) form one of both with R and it was impossible for me. It is driving me mad!

If someone could help me, or tell me something about this, I'd be very gratefull!

Thanks in advance.

Jane M · 03-22-2012, 03:47 AM

One idea is to keep only the mutations in which you are interested by using a bash script, for example somatic or LOH.
But if you are interested in germline mutations, you won't maybe be able to read everything in R because that are the more frequent mutations...

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03-22-2012, 02:37 AM	#1
pablosantamarta Junior Member Location: Spain Join Date: Mar 2012 Posts: 1	How to plot datasets from VarScan2 in R. Hi everybody, I'm using VarScan2's Somatic Mutation Calling function and the output are two files with a large number of columns. I wanna represent graphically two columns (normal_var_freq(column 7) and tumor_var_freq(column 11)) form one of both with R and it was impossible for me. It is driving me mad! If someone could help me, or tell me something about this, I'd be very gratefull! Thanks in advance.

03-22-2012, 03:47 AM	#2
Jane M Senior Member Location: Paris Join Date: Aug 2011 Posts: 239	One idea is to keep only the mutations in which you are interested by using a bash script, for example somatic or LOH. But if you are interested in germline mutations, you won't maybe be able to read everything in R because that are the more frequent mutations...