Hi,

For cases where strand matters in your analysis, I would suggest moving away
from RangedData (which knows nothing about biology) to GRanges.

gr <- as(rd, "GRanges")
reduce(gr)

Should get you somewhere close.

Michael

On Thu, Apr 1, 2010 at 9:53 AM, Kunbin Qu <KQu@genomichealth.com> wrote:

> Hi,
>
> I have a RangedData object lib1RD like the following, space as the
> chromosome name: 18S, chr1, chr2 etc. and it has two values: strand and
> index. I'd like to cluster (by using "reduce") all the reads on the same
> strand from each chromosome. Could you help me on how to extract the
> reads for each chromosome with the same strand enforcement?
>
> Like    reduce(ranges(lib1RD)$"18S"[strand == '-'] something like this?
>
> Thanks a lot.
>
> -Kunbin Qu
>
>
>
> > lib1RD
> RangedData with 4982872 rows and 2 value columns across 28 spaces
>         space       ranges |   strand     index
>   <character>    <IRanges> | <factor> <integer>
> 1          18S [ 537,  568] |        -         5
> 2          18S [  51,   73] |        -        19
> 3          18S [  47,   78] |        -        52
> 4          18S [1548, 1568] |        -        64
> 5          18S [1727, 1758] |        +       111
> 6          18S [1164, 1195] |        +       121
> 7          18S [1791, 1819] |        -       123
> 8          18S [ 830,  853] |        -       158
> 9          18S [1713, 1744] |        -       165
> 10         18S [ 199,  228] |        -       175
> ...
> <4982862 more rows>
> >
>
> ______________________________________________________________________
> The contents of this electronic message, including any attachments, are
> intended only for the use of the individual or entity to which they are
> addressed and may contain confidential information. If you are not the
> intended recipient, you are hereby notified that any use, dissemination,
> distribution, or copying of this message or any attachment is strictly
> prohibited. If you have received this transmission in error, please send an
> e-mail to postmaster@genomichealth.com and delete this message, along with
> any attachments, from your computer.
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

	[[alternative HTML version deleted]]

