[BioC] multicore and GRangesList

[Stefano Calza]

Hi,

you cannot do that. lapply, sapply, ecc. methods for GRangesLists are specific, not standard ones.

I've been using it but afaik requires some hacking (unless you coerce the object to a list, which took long time for me...and didn't like).

maybe someone has better suggestion

Stefano

On Tue, Jan 11, 2011 at 03:34:46PM +0100, arne.mueller at novartis.com wrote:
<arne.mueller>Dear All,
<arne.mueller>
<arne.mueller>Has anybody experience using the multicore package with GRangesLists from 
<arne.mueller>the GenomicRanges package? I can't get it working ..., here's an example:
<arne.mueller>
<arne.mueller>> a = GRanges(seqnames="A", ranges=IRanges(start=1:3, width=5))
<arne.mueller>> b = GRanges(seqnames="A", ranges=IRanges(start=c(10,20,30), width=5))
<arne.mueller>> grl = GRangesList(a, b)
<arne.mueller>> sapply(grl, length)
<arne.mueller>[1] 3 3
<arne.mueller>> mclapply(grl, length, mc.cores=2)
<arne.mueller>[[1]]
<arne.mueller>[1] "Error in as.list.default(X) : \n  no method for coercing this S4 
<arne.mueller>class to a vector\n"
<arne.mueller>
<arne.mueller>[[2]]
<arne.mueller>[1] "Error in as.list.default(X) : \n  no method for coercing this S4 
<arne.mueller>class to a vector\n"
<arne.mueller>
<arne.mueller>
<arne.mueller>> sessionInfo()
<arne.mueller>R version 2.13.0 Under development (unstable) (2010-12-20 r53870)
<arne.mueller>Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
<arne.mueller>
<arne.mueller>locale:
<arne.mueller>[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
<arne.mueller>
<arne.mueller>attached base packages:
<arne.mueller>[1] stats     graphics  grDevices utils     datasets  methods   base 
<arne.mueller>
<arne.mueller>other attached packages:
<arne.mueller>[1] multicore_0.1-3     GenomicRanges_1.3.7 IRanges_1.9.17 
<arne.mueller>
<arne.mueller>loaded via a namespace (and not attached):
<arne.mueller>[1] tools_2.13.0
<arne.mueller>
<arne.mueller>    thanks a lot for hints ..
<arne.mueller>
<arne.mueller>   arne
<arne.mueller>	[[alternative HTML version deleted]]
<arne.mueller>
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-- 
Stefano Calza, PhD
Researcher/Assistent Professor - Biostatistician

*Sezione di Statistica Medica e Biometria
 Dipartimento di Scienze Biomediche e Biotecnologie
 Università degli Studi di Brescia - Italy
 Viale Europa, 11 25123 Brescia

 email: stefano.calza at med.unibs.it
        stefano.calza at biostatistics.it

 pec: stefano.calza at pec.biostatistics.it

 Phone: +390303717653
 Fax: +390303717488