Hi Everyone,
This is my first attempt in R/bioconductor outside of plot()/hist()
function. Thanks to Martin Morgan, I was impressed with what
bioconductor can do for me ( after attending bioc workshop last week).

When I try to findOverlap on two GFF files I get information on which
feature is overlapping with another feature. But, instead of using "feature
names" it just indicates 1,2, 3...etc. Is there a way, i can make it output
gene names. (my GRanges objects are read from gff files using Rtracklayer &
later have names (geneids) assigned to them using names() function).

> findOverlaps(au, am)
Hits of length 1740
queryLength: 790
subjectLength: 1054
     queryHits subjectHits
      <integer>   <integer>
 1            1           1
 2            1         528
 3            2          13
 4            2         540
 5            3         136



And here is the background of what i am trying to do. In case, if any of
you have a better suggestion:
I run 3 de novo gene prediction algorithm on our newly assembled genome.
And I would like to reconcile the gene sets from all of them to genes (a)
predicted with exact same boundaries in all three (b) boundaries not same
but overlap (c) predicted by only one or two of them.

And use reduce in case of (b) to obtain outer most boundaries of
overlapping prediction.

As a novice users its bit overwhelming for me.

Thanks very much,
Gowthaman

-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).

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