[Bioc-sig-seq] weird interaction between BSgenome (getSeq) and ChIPpeakAnno
Ivan Gregoretti
ivangreg at gmail.com
Thu Feb 24 16:11:26 CET 2011
Hello Janet.
First, we are not tired of your posts. For instance, your catch of the
bug in the reduce() function will save hours of frustration for many
users. Thank you.
Second, the getSeq() problem that you find after loading ChIPpeakAnno
seems to be solved in the devel branch (see sessionInfo below). I
tested it following your steps but with BSgenome.Mmusculus.UCSC.mm9.
Not that it actually matters but I chose this genome because it has 3
million Ns at the beginning of every chromosome (except chrY).
I hope this helps.
Ivan
########################################################
> sessionInfo()
R version 2.13.0 Under development (unstable) (2010-12-02 r53747)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPpeakAnno_1.7.0 limma_3.7.23
[3] org.Hs.eg.db_2.4.6 GO.db_2.4.5
[5] RSQLite_0.9-4 DBI_0.2-5
[7] AnnotationDbi_1.13.13 BSgenome.Ecoli.NCBI.20080805_1.3.17
[9] multtest_2.7.1 Biobase_2.11.8
[11] biomaRt_2.7.1 BSgenome.Mmusculus.UCSC.mm9_1.3.17
[13] BSgenome_1.19.3 Biostrings_2.19.9
[15] GenomicRanges_1.3.18 IRanges_1.9.22
loaded via a namespace (and not attached):
[1] MASS_7.3-11 RCurl_1.5-0 splines_2.13.0 survival_2.36-5
[5] XML_3.2-0
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 Wed, Feb 23, 2011 at 7:06 PM, Janet Young <jayoung at fhcrc.org> wrote:
> Hi again,
>
> (sorry, you're probably tired of hearing from me now).
>
> I have just started to play with ChIPpeakAnno - it looks like it might be very useful for me. However, once I load it I get an error from BSgenome's getSeq function. Here's the error alone (myregions_RD is a RangedData object), and below is my full code.
>
> getSeq(Cfamiliaris,myregions_RD)
> Error in x[[name, exact = FALSE]] :
> missing '[[' method for Sequence class GRanges
>
>
> thanks (yet again),
>
> Janet
>
> -------------------------------------------------------------------
>
> Dr. Janet Young (Trask lab)
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., C3-168,
> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>
> tel: (206) 667 1471 fax: (206) 667 6524
> email: jayoung ...at... fhcrc.org
>
> http://www.fhcrc.org/labs/trask/
>
> -------------------------------------------------------------------
>
>
>
>
> R version 2.12.1 (2010-12-16)
> Copyright (C) 2010 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
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> Type 'contributors()' for more information and
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>
> Type 'demo()' for some demos, 'help()' for on-line help, or
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> Type 'q()' to quit R.
>
>> library(IRanges)
>
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
> cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin,
> pmin.int, rbind, rep.int, table
>
>
>
>> library(BSgenome.Cfamiliaris.UCSC.canFam2)
> Loading required package: BSgenome
> Loading required package: GenomicRanges
> Loading required package: Biostrings
>
>> myregions_RD <- RangedData(IRanges(start=c(100001L,2000001L),end=c(100100L,2000100L)),space=c("chr1","chr2"),strand=c("+","+") )
>
>> getSeq(Cfamiliaris,myregions_RD)
> [1] "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
> [2] "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
>
>> library(ChIPpeakAnno)
> Loading required package: biomaRt
> Loading required package: multtest
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>
> Attaching package: 'Biobase'
>
> The following object(s) are masked from 'package:IRanges':
>
> updateObject
>
> Loading required package: BSgenome.Ecoli.NCBI.20080805
> Loading required package: GO.db
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: org.Hs.eg.db
> Loading required package: limma
>
>> getSeq(Cfamiliaris,myregions_RD)
> Error in x[[name, exact = FALSE]] :
> missing '[[' method for Sequence class GRanges
>
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] ChIPpeakAnno_1.6.0
> [2] limma_3.6.9
> [3] org.Hs.eg.db_2.4.6
> [4] GO.db_2.4.5
> [5] RSQLite_0.9-4
> [6] DBI_0.2-5
> [7] AnnotationDbi_1.12.0
> [8] BSgenome.Ecoli.NCBI.20080805_1.3.16
> [9] multtest_2.7.1
> [10] Biobase_2.10.0
> [11] biomaRt_2.6.0
> [12] BSgenome.Cfamiliaris.UCSC.canFam2_1.3.16
> [13] BSgenome_1.18.3
> [14] Biostrings_2.18.2
> [15] GenomicRanges_1.2.3
> [16] IRanges_1.8.9
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-11 RCurl_1.5-0 splines_2.12.1 survival_2.36-5
> [5] XML_3.2-0
>
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