[BioC] Curious file size issues

Daniel Brewer daniel.brewer at icr.ac.uk
Thu Mar 12 11:28:35 CET 2009


The GTF file from Ensembl for the human genome,
Homo_sapiens.NCBI36.52.gtf, is 194M and is a tab-delimted text file.  I
import it into R and process it so that there are two objects:
genomeRanges & genomeBlocks.  genomeRanges is a list of IRanges objects,
each of which is a particular chromosome and strand.  genomeBlocks is a
list of dataframes with the associated annotation for each of the

When I save this to file
(save(genomeBlocks,genomeRanges,file="Hsgenome.Rdata")) it comes out as
859M.  How is this possible? Especially as the Rdata file is a binary

> object.size(genomeBlocks)
[1] 2939935864

> object.size(genomeRanges)
[1] 8769208

Anyway got any ideas what is going on?



Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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