[BioC] Cleaning up after getSeq(BSgenome, GRanges)

[Steve Lianoglou]

Howdy,

Say I'd like to fetch muchos sequences from hg19 that are defined in a
GRanges object that spans all hg19 chromosomes.

I can make my life easy and do:

R> library(BSgenome.Hsapiens.UCSC.hg19)
R> seqs <- getSeq(Hsapiens, my.GRanges)

But while my life has been made easy, life for my CPU has been made
harder as I (think that I) have now all of the Hsapiens chromosomes
loaded up into (I think) the Hsapiens at .seqs_cache.

I reckon I can do something like:

R> rm(list=ls(Hsapiens at .seqs_cache), envir=Hsapiens at .seqs_cache)
R> gc()

to try to remedy the situation myself, but I wonder if I'm missing
something else?

Perhaps having a clearCache,BSgenome method to do some cleanup might be handy?

Thanks,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact