On Thu, May 14, 2009 at 4:29 PM, Kasper Daniel Hansen <
khansen@stat.berkeley.edu> wrote:

> As far as I know USCS uses zero-based indexing of their genomes, R uses
> 1-based. What kind of conversion is being used by rtracklayer - I suspect
> none at all?


The indexing is 1-based. rtracklayer takes care of all of this (0 vs 1
based, closed vs half-open) behind the scenes. I've found places where I've
messed up before though, so please let me know if you find inconsistencies.


> It might be worthwhile to add a discussion about this somewhere in the
> vignette?
>

Yes, it should be mentioned.


> More specifically, I have downloaded a couple of tables from UCSC using
> rtracklayer and I wanted to know if I need to add 1 to the column named
> exonStart (after a suitable splitting - it is a comma separated character
> list).
>

If you download a table (not an actual RangedData track), then the columns
have not been adjusted at all. I suggest you everything 1-based and closed
if you want to use it with packages like IRanges and Biostrings.

Btw, if you had obtained the data using the track() function, which returns
a RangedData, you could call blocks() on it to get the block information as
a RangesList. But I just found that I forgot to add 1 in that method; fixed
in svn.

Thanks,
Michael


> Kasper
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

