On Thu, Mar 22, 2012 at 5:36 PM, Javerjung Sandhu <jsandhu@bcgsc.ca> wrote:

> Dear Sir or Madam,
>
> I am interested in using Bioconductor to analyze and compare some data
> I’ve recently acquired and was wondering if you could help direct me to an
> appropriate analysis package.
>
>
I have two sets of data, from two separate groups of AML patients.  One set
> is of 96 patients, the other set is of 178 patients, and I have sequencing
> data for both groups.  For a few genes of interest the first group’s
> dataset, it looked like there were a number of SNPs that were found with a
> higher than normal frequency among the 96 patients. What I would like to do
> is find out if the frequency of these SNPs is the same in the dataset of
> 178 patients.  I just need a way of analyzing the frequency of SNPs in a
> large set of sequences.
>

This question is not very clear.  If you have already done SNP calling with
your sequences (using samtools or some other external resource) I suppose
it would be typical to have results in VCF format.  This can be parsed
using VariantAnnotation package, and you can tabulate variants and do some
kind of categorical analysis to compare populations downstream. Some of the
relevant computations for variant tabulation on the basis of VCF are given
in the cgdv17 experimental data package vignette.  There are no high level
functions that I know of for doing population comparisons, so you should
involve an experienced statistical geneticist if possible.

If you have not done SNP calling, and your sequence data are in SAM or BAM
format, you could use the pileup manipulations of Rsamtools to enumerate
and tabulate variants.  Examples of such manipulations in the domain of
transcript variants can be found in the vignette of the ggtut experimental
data package.


> Thanks very much,
> Jung
>
>
>
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