[BioC] Hypergeometric test

[Steve Lianoglou]

Hi,

On Thu, Nov 21, 2013 at 12:53 AM, amit kumar subudhi
<amit4help at gmail.com> wrote:
> Hi All,
>
> Can any one suggest me the procedure/software to conduct Hypergeometric
> test on my gene list? I have a list of deferentially regulated genes and
> list of sets of genes involved in common biological process , function and
> cellular component.
> I have done part of it using BINGO and DAVID but I need to perform this on
> my own gene set that I have made in a way to answer my specific research
> question.

The GOstats package can help you here:
http://www.bioconductor.org/packages/2.13/bioc/html/GOstats.html

You could either go "whole hog" and follow the instructions in the
"Hypergeometric tests for less common model organisms" vignette, or
simply just rig up your own hyper-geometric tests in a more "manual"
way via the `phyper` function.

If you browse through the source of the "Hypergeometric Tests Using
GOstats" vignette there, you will even see a small function that shows
you how to use it, the relevant bits being:

phyper(numFound-1, numAtCat, numNotAtCat, numDrawn, lower.tail=FALSE)

The var names used here combined with the help in ?phyper should get
you where you need to go.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech