[BioC] regarding makeTranscriptDbFromGFF

[Steve Lianoglou]

Hi,

On Thu, Sep 26, 2013 at 9:07 PM, deepika lakhwani
<lakhwanideepika at gmail.com> wrote:
> Hii...
>
> Ok, i got it. Actually i was thinking warning message also an error and yes
> its a fuctional txdb and trying so many fuctions and it works.If i want to
> add chromosome information then what should i do. I am trying but it did
> not work.
> I am learning these new things so apologize for asking very basic question.

A great deal of effort has been put into the documentation for many of
the packages you will find through bioconductor, this is especially
true for the "foundational" packages -- and GenomicFeatures is one
such package.

GenomicFeatures is based on GenomicRanges, which in turn is based on IRanges.

Please read through the vignettes for these packages which are the
PDFs you'll find in the pages for each package under the
"Documentation" section here with a mind to really understand them
(not just skim the pages):

http://bioconductor.org/packages/release/bioc/html/IRanges.html
http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html

It's better to understand how these things work on a more fundamental
level than to repeatedly ask for help with superficial issues until
what you want magically works. It might feel slower to get going, but
your terminal velocity will be a lot higher than you'll hit than not
gaining this understanding in the first place.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech