[Bioc-sig-seq] using value in RangedData

[Charles C. Berry]

On Thu, 1 Apr 2010, Kunbin Qu 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?

 	reduce(ranges(subset( lib1RD, strand== '-' )))

HTH,

Chuck


>
> 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>
>>
>
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Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901