[BioC] SomaticSignatures

Steve Lianoglou lianoglou.steve at gene.com
Thu Mar 27 21:34:01 CET 2014


On 27 Mar 2014, at 13:01, Huma Asif wrote:

> Hi
> Though i installed variant annotation and R vesion as suggested. every 
> package seems dependent on other like somatic signature 
> ....mutationcontext..... variantannotation......GRanges....h5vc 
> package.

That's why installation functions (like biocLite) are made available. 
They handle the dependency chasing for you.

> It seems impossible

It's not impossible, you just need to do a lot of book keeping regarding 
the dependency structure of the packages SomaticSignatures depends on 
(and the packages those packages depend on) if you insist on installing 
this manually.

Why is installing it via `biocLite('SomaticSignatures')` out of the 
question here? You obviously have access to an internet connection -- 
you are sending email and downloading the dependent packages by hand -- 
so, why don't you just install it that way?

> I need  to know is there any other package that can help in 
> signatures extraction from vcf files with out being dependent on R.

It looks like they are "just" creating a variant-by-sample matrix and 
performing some matrix decomposition on that (SVD, NMF), so if you know 
how to do each one of these things individually that does not involve R, 
then you're in business.


Steve Lianoglou
Computational Biologist

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