[BioC] [devteam-bioc] apply function on genomicsRanges ob

[Valerie Obenchain]

Hi,

I think you mean the GRanges class. GenomicRanges is a virtual class, 
GRanges is the concrete subclass.

Please show a reproducable example of what you're trying to do. When you 
provide an example, instead of asking for a apply function for GRanges, 
others on the list can see what the end goal is and suggest 
alternatives. Using an *apply function may not be the best approach.

Valerie


On 06/26/2014 06:41 AM, Maintainer wrote:
> Hello,
>
> Does the apply function exist for genomisRange object. Here , I don't talk about a genomicRangesList object but genomic Range.
> Is it pertinent to implement it ?
>
> Actually, I populate my gr object with a for loops : depending the position of the gene , I had some information in mcol( gr obj).
> unsurprising, the for loop is totally unefficient.
>
> Greg.
> Lady Davis Institute
> Montreal
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] ade4_1.6-2          IRanges_1.20.7      BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
> [1] stats4_3.0.1 tools_3.0.1
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> ________________________________________________________________________
> devteam-bioc mailing list
> To unsubscribe from this mailing list send a blank email to
> devteam-bioc-leave at lists.fhcrc.org
> You can also unsubscribe or change your personal options at
> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc
>


-- 
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fhcrc.org
Phone: (206) 667-3158