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I want to load a GFF (annotation) file into an R data frame in order to extract some information from it, e.g. the location of transposons in the genome.

I used the following code:

library(rtracklayer)
gff <- rtracklayer::import('c_elegans.PRJNA13758.WS263.annotations.gff3.gz')
Error: cannot allocate vector of size 210.2 Mb

It seems that the GFF3 file is too big for loading into R. Do you know if this is limited by R or by my computer's memory?

I ran this on a GNU/Linux computer.

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1 Answer 1

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It depends of course on your available RAM on your computer.

Under Windows you can increase the available RAM in R with memory limit:

> memory.limit()
[1] 8070
> memory.limit(size=10000)
[1] 10000
> memory.limit()
[1] 10000

But that is not necessary on linux/unix.

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    $\begingroup$ This only works (and is only required) on Windows. OP is using Linux. Not sure why he accepted this answer. $\endgroup$
    – Konrad Rudolph
    May 20, 2018 at 12:39
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    $\begingroup$ Indeed, memory.limit() [1] Inf Warning message: 'memory.limit()' is Windows-specific. I understood this as 'no memory limit' on Linux, so only limited by available RAM? $\endgroup$
    – Biomagician
    May 21, 2018 at 0:17

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