[BioC] saving GRanges objects - resulting file size issue
Valerie Obenchain
vobencha at fhcrc.org
Mon Aug 19 15:40:27 CEST 2013
Hi Andrew,
I can't reproduce this problem. Can you successfully save the files in a
different order, i.e., is it just the addition of 'introns' that is
giving you trouble?
I assume these are custom annotation GRanges that did not come from a
TxDb in Bioconductor. Can you make the files available for testing?
Valerie
On 08/16/2013 10:13 AM, Andrew Jaffe wrote:
> Hey,
>
> I'm trying to save several GRanges objects in the same rda file, but for
> some reason, one of the smaller GRanges objects (~23Mb) makes the saved
> file go from 25Mb to 9Gb+ and I'm unsure of why exactly, and have never
> seen this problem before:
>
>> class(exons)
> [1] "GRanges"
> attr(,"package")
> [1] "GenomicRanges"
>> class(utr5seg)
> [1] "GRanges"
> attr(,"package")
> [1] "GenomicRanges"
>> class(utr3seg)
> [1] "GRanges"
> attr(,"package")
> [1] "GenomicRanges"
>> class(introns)
> [1] "GRanges"
> attr(,"package")
> [1] "GenomicRanges"
>> save(exons, utr5seg, utr3seg, trans, tInfo, t2g, # introns,
> file="annotation-tables-forRNAseq.rda")
>
> the resulting saved object size in my directory is 23mb
>
>> print(object.size(introns),units="Mb")
> 22.9 Mb
>
> but when i include this `introns` GRanges object by running:
>
> save(exons, utr5seg, utr3seg, trans, tInfo, t2g, introns,
> file="annotation-tables-forRNAseq.rda")
>
> the object size in my directory got up to 9Gb, and I have to kill the save.
> any idea whats going on??
>
>> introns
> GRanges with 691807 ranges and 2 metadata columns:
> seqnames ranges strand | tx_id
> <Rle> <IRanges> <Rle> | <character>
> [1] chr1 [ 12228, 12645] + | 1,2,3
> [2] chr1 [ 12698, 13402] + | 1,2,3
> [3] chr1 [322229, 324287] + | 7
> [4] chr1 [324346, 324438] + | 7
> [5] chr1 [324061, 324287] + | 8
> ... ... ... ... ... ...
> [691803] chrY [27216989, 27218792] - | 76941
> [691804] chrY [27218869, 27245878] - | 76941
> [691805] chrY [27329896, 27330860] - | 76942
> [691806] chrY [59359509, 59360006] - | 76950
> [691807] chrY [59360116, 59360500] - | 76950
> tx_name
> <character>
> [1] uc001aaa.3,uc010nxq.1,uc010nxr.1
> [2] uc001aaa.3,uc010nxq.1,uc010nxr.1
> [3] uc009vjk.2
> [4] uc009vjk.2
> [5] uc001aau.3
> ... ...
> [691803] uc011nbv.2
> [691804] uc011nbv.2
> [691805] uc004fwt.3
> [691806] uc011ncc.1
> [691807] uc011ncc.1
> ---
> seqlengths:
> chr1 chr2 chr3 chr4 ... chr22 chrX chrY
> 249250621 243199373 198022430 191154276 ... 51304566 155270560 59373566
>
>
> Thanks a ton,
> Andrew
>
> [[alternative HTML version deleted]]
>
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