[BioC] SomaticSignatures

[Steve Lianoglou]

Hi,

On 24 Mar 2014, at 12:02, Huma Asif wrote:

> Hi
> Is there any other way to install Somatic signature if not via 
> biocLite
> Do you  means i have to wait till April to use this Package.

You could always install the current working version of 3.1-dev -- this 
is very easy to do on OSX and probably equally easy on other platforms 
(except windows, of course ;-) if you are comfortable doing some basic 
sys-admin type of tasks.

What system are you on?

> Though i have downloaded and unzip the package but dont know how to 
> proceed next.

you downloaded the source package?

> in document it says
> The starting point of the analysis is a VRanges object which describes 
> the somatic variants in terms of their genomic locations as well as 
> reference and alternative alleles
>
> so do i need to install VariantAnnotation  also 
> Sorry if it sounds stupid 

You will have to install every package listed in the Imports and Depends 
fields that you see on the package's home page.

All of those can be installed in  your current version of R easily via 
biocLite

If you insist on installing this package into your current working 
version of R (after you installed the dependent packages), you may be 
able to do so if it doesn't depend on functionality coming in bioc2.14 
that's not in bioc2.13 -- I have no idea of knowing the answer to that.

If I were you, I'd install a working version of R-devel and all of the 
packages from bioc2.14 -- which will happen automatically when  you use 
biocLite.

If you search the mailing lists, the question of how to do this (with 
answers) appears often here -- read through several of these threads in 
their entirety so you avoid tripping over some gotcha's that may bite 
you in the process.

Having multiple working versions of R (current and devel) is ultimately 
pretty easy (assuming you know how to do it ;-). Depending on your level 
of sys-admin savvy it can be anywhere from a 30 minute "thing" to a 
multiple day endeavor.

HTH,
-steve