> I am a Post-doc student started analyzing human genome data few days
> back. My aim is to find UVA signature mutations. i have done variant
> calling by GATK and was wondering how i can extract signatures using
> these call without using much programming (as I am a biologist
> in Bioinformatics field). while doing search on web i came
> across Package ???SomaticSignatures???. i have some questions
> can you please suggest what can help me in handling this package?
> My first aim is to use my data and find sequence context of these
> please suggest me any easy guide to start with
-- output of sessionInfo():
R version 3.0.3 (2014-03-06)
Platform: i686-pc-linux-gnu (32-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=en_US.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
Sent via the guest posting facility at bioconductor.org.
On Sat, Mar 22, 2014 at 2:13 PM, hasif [guest] <guest at="" bioconductor.org=""> wrote:
> Hi there,
>> I am a Post-doc student started analyzing human genome data few
>> back. My aim is to find UVA signature mutations. i have done
>> calling by GATK and was wondering how i can extract signatures
>> these call without using much programming (as I am a biologist
>> in Bioinformatics field). while doing search on web i came
>> across Package ? EURO ~SomaticSignatures? EURO (tm). i have some
>> can you please suggest what can help me in handling this package?
>> My first aim is to use my data and find sequence context of these
>> please suggest me any easy guide to start with
Have you read through the rather extensive looking vignette?
First: please keep all correspondence on-list (by replying with
"Reply-All") so that other can help as well as benefit from
Other comments inline:
On 24 Mar 2014, at 6:32, Huma Asif wrote:
> i have read that just but i have to get my machine ready first so i
> can apply the instruction in that?
> i am doing this and got this message
> Warning messages:
> 1: package ?SomaticSignatures? is not available (for R version
It looks like this package is only available in bioc-devel, which has
not been released yet.
How would you have known?
It will be released sometime in April (I believe) after R-3.1.x is
released. In order for you to install SomaticSignatures via biocLite,
you have to first install the current development version of R-3.1.
> 2: installed directory not writable, cannot update packages
> ? 'KernSmooth', 'rpart', 'spatial'
It also looks like you are running R as a user who does not have
to install into the default package directory. You can either run R as
administrator account, or setup a package directory in your home
directory that R can use "on top of" the default install. To figure
how to do that, google "r_libs_user"