On Wed, Mar 9, 2011 at 6:41 AM, Ivan Gregoretti <[email protected]> wrote:
> Just to expand a little bit Vincent's response.
>
> If you happen to be handling very large BED files, you probably keep
> them compressed. The good news is that even in that case, you can load
> them:
>
> lit = import("~/lit.bed.gz"."bed")
>
> There is still the long-standing issue of how slow the import()
> function is but I am still hopeful.
>
>
This is the first I've heard of this. What sort of files are slow? Do they
have a track line? The parsing gets complicated when there are track lines
and multiple tracks in a file. BED is a complex format with many variants.
> Ivan
>
> Ivan Gregoretti, PhD
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> 5 Memorial Dr, Building 5, Room 205.
> Bethesda, MD 20892. USA.
> Phone: 1-301-496-1016 and 1-301-496-1592
> Fax: 1-301-496-9878
>
>
>
> On Tue, Mar 8, 2011 at 9:26 PM, Vincent Carey
> <[email protected]> wrote:
> > 2011/3/8 Thiago Yukio Kikuchi Oliveira <[email protected]>:
> >> Hi,
> >>
> >> Is there a BED file parser for R?
> >
> > I suppose it depends on what you mean by "parser". import() from the
> > rtracklayer package imports BED and constructs and populates a
> > RangedData object with the contents. Here we look at a small bed file
> > in text,
> > start R, load rtracklayer, import the data, show the result, and show
> > the resources used.
> >
> > bash-3.2$ head ~/junc716_20.bed
> > chr20 55658 64827 JUNC00000001 14 + 55658 64827
> > 255,0,0 2 27,25 0,9144
> > chr20 55662 64821 JUNC00000002 2 - 55662 64821
> > 255,0,0 2 34,8 0,9151
> > chr20 135774 147029 JUNC00000003 1 - 135774 147029
> > 255,0,0 2 8,29 0,11226
> > chr20 167951 172361 JUNC00000004 1 + 167951 172361
> > 255,0,0 2 29,8 0,4402
> > chr20 189824 192113 JUNC00000005 3 + 189824 192113
> > 255,0,0 2 33,9 0,2280
> > chr20 189829 192113 JUNC00000006 3 + 189829 192113
> > 255,0,0 2 32,9 0,2275
> > chr20 193930 199576 JUNC00000007 4 - 193930 199576
> > 255,0,0 2 28,11 0,5635
> > chr20 207050 207846 JUNC00000008 2 - 207050 207846
> > 255,0,0 2 20,34 0,762
> > chr20 218306 218925 JUNC00000009 1 - 218306 218925
> > 255,0,0 2 11,26 0,593
> > chr20 221160 225070 JUNC00000010 25 - 221160 225070
> > 255,0,0 2 29,9 0,3901
> > bash-3.2$ head ~/junc716_20.bed > ~/lit.bed
> > bash-3.2$ R213 --vanilla --quiet
> >> library(rtracklayer)
> > Loading required package: RCurl
> > Loading required package: bitops
> >> lit = import("~/lit.bed")
> >> lit
> > RangedData with 10 rows and 9 value columns across 1 space
> > space ranges | name score strand
> thickStart
> > <character> <IRanges> | <character> <numeric> <character>
> <integer>
> > 1 chr20 [ 55659, 64827] | JUNC00000001 14 +
> 55658
> > 2 chr20 [ 55663, 64821] | JUNC00000002 2 -
> 55662
> > 3 chr20 [135775, 147029] | JUNC00000003 1 -
> 135774
> > 4 chr20 [167952, 172361] | JUNC00000004 1 +
> 167951
> > 5 chr20 [189825, 192113] | JUNC00000005 3 +
> 189824
> > 6 chr20 [189830, 192113] | JUNC00000006 3 +
> 189829
> > 7 chr20 [193931, 199576] | JUNC00000007 4 -
> 193930
> > 8 chr20 [207051, 207846] | JUNC00000008 2 -
> 207050
> > 9 chr20 [218307, 218925] | JUNC00000009 1 -
> 218306
> > 10 chr20 [221161, 225070] | JUNC00000010 25 -
> 221160
> > thickEnd itemRgb blockCount blockSizes blockStarts
> > <integer> <character> <integer> <character> <character>
> > 1 64827 #FF0000 2 27,25 0,9144
> > 2 64821 #FF0000 2 34,8 0,9151
> > 3 147029 #FF0000 2 8,29 0,11226
> > 4 172361 #FF0000 2 29,8 0,4402
> > 5 192113 #FF0000 2 33,9 0,2280
> > 6 192113 #FF0000 2 32,9 0,2275
> > 7 199576 #FF0000 2 28,11 0,5635
> > 8 207846 #FF0000 2 20,34 0,762
> > 9 218925 #FF0000 2 11,26 0,593
> > 10 225070 #FF0000 2 29,9 0,3901
> >
> >> sessionInfo()
> > R version 2.13.0 Under development (unstable) (2011-03-01 r54628)
> > Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit)
> >
> > locale:
> > [1] C
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > other attached packages:
> > [1] rtracklayer_1.11.11 RCurl_1.5-0 bitops_1.0-4.1
> >
> > loaded via a namespace (and not attached):
> > [1] BSgenome_1.19.4 Biobase_2.11.9 Biostrings_2.19.15
> > [4] GenomicRanges_1.3.23 IRanges_1.9.25 Matrix_0.999375-47
> > [7] XML_3.2-0 grid_2.13.0 lattice_0.19-17
> >
> >
> >>
> >>
> >> Thanks
> >>
> >> / Thiago Yukio Kikuchi Oliveira
> >> (=\
> >> \=) Faculdade de Medicina de Ribeirão Preto
> >> / Laboratório de Genética Molecular e Bioinformática
> >> /=) -----------------------------------------------------------------
> >> (=/ Centro de Terapia Celular/CEPID/FAPESP - Hemocentro de Rib. Preto
> >> / Rua Tenente Catão Roxo, 2501 CEP 14151-140
> >> (=\ Ribeirão Preto - São Paulo
> >> \=) Fone: 55 16 2101-9300 Ramal: 9603
> >> / E-mail: [email protected]
> >> /=) [email protected]
> >> (=/
> >> / Bioinformatic Team - BiT: http://lgmb.fmrp.usp.br
> >> (=\ Hemocentro de Ribeirão Preto: http://pegasus.fmrp.usp.br
> >> \=)
> >> / -----------------------------------------------------------------
> >>
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> >>
> >
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