Hello,
For a not so large list of GRanges:
> length(blockRanges)
[1] 4029
> class(blockRanges)
[1] "list"
Which don't have an unreasonable number of elements in them:
> summary(sapply(blockRanges, length))
Min. 1st Qu. Median Mean 3rd Qu. Max.
1 961 20710 55210 77680 759600
Combining them takes 15 minutes:
> system.time(allRanges <- do.call(c, blockRanges))
sessionInfo()
user system elapsed
935.770 23.657 961.952
> head(blockRanges[[1]])
GRanges with 6 ranges and 1 metadata column:
seqnames ranges strand | conservation
<Rle> <IRanges> <Rle> | <numeric>
[1] chr1 [10918, 10918] * | 0.064
[2] chr1 [10919, 10919] * | 0.056
[3] chr1 [10920, 10920] * | 0.064
[4] chr1 [10921, 10921] * | 0.056
[5] chr1 [10922, 10922] * | 0.064
[6] chr1 [10923, 10923] * | 0.064
---
seqlengths:
chr1
NA
Could this code be faster ?
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
other attached packages:
[1] GenomicRanges_1.10.5 IRanges_1.16.4 BiocGenerics_0.4.0
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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