[BioC] function precede() not working with GRanges

[Steve Lianoglou]

Hi,

2011/1/12 Michael Lawrence <lawrence.michael at gene.com>:
[snip]
> Time will tell, I guess. Anyway, let's not make
> GenomicRanges the RNA-seq package.

Yeah, let's not do that, but let's also keep the strand-awaredness.

Not that I think you're arguing to ignore it, I just wanted to let it
be known that I like it's ability to do so.

I didn't see your email last night before sending off the one I sent,
and I think your suggestion of including a param to the 'strand-aware'
function that flip their ability to honor/ignore strand (default to
honoring strand) is a great idea.

> Suffice it to say that we deal RNA-seq,
> ChIP-seq, other DNA-seqs and up till now we always need to remove strand
> before looking for overlaps.

I typically deal with this right from the get-go as I read data from
my BAM files. If I know the data is coming from a non-stranded
protocol, I just set the strand to '*' as I'm building up my GRanges
objects from the scanBam results ...

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact