On Mon, Feb 8, 2010 at 6:59 AM, [email protected] <
[email protected]> wrote:
> Dear bioc-sig-sequencing,
>
> 1. I would like to annotate (& graphically display in context of genome
> annotation) ChIP-Seq peaks found using Arabidopsis samples. Can someone
> comment on practical way(s) to do this?
>
>
To get your peaks, yes you would use IRanges and end up with a RangedData.
For graphics, there's the GenomeGraphs package, which uses biomaRt for
annotations. But biomaRt is not designed to efficiently find the annotations
that intersect with your peaks. For that, ChIPpeakAnno and IRanges + e.g.
GenomicFeatures can help.
Normally I would recommend rtracklayer for a simple visualization, but I
don't think UCSC supports Arabidopsis.
> 2. For example, would the following be an appropriate approach:
>
> a. Employ ChIPpeakAnno package?
>
> b. For my ChIPSeq peaks data, would format as RangedData as page 10 of
> BasicChIPSeq.pdf handout for 11/19/09 talk of M. Morgan (for Nov. 18-20
> conference, Seattle)?
>
> 2. Can you comment on the error message below?
>
>
> > library(ChIPpeakAnno)
> ...
> > library("biomaRt")
> > listMarts()
> biomart
> 1 ensembl
> 2 snp
> 3 functional_genomics
> 4 vega
> 5 msd
> 6 bacterial_mart_3
> 7 fungal_mart_3
> 8 metazoa_mart_3
> 9 plant_mart_3
> ...
> version
> 1 ENSEMBL 56 GENES (SANGER UK)
> 2 ENSEMBL 56 VARIATION (SANGER UK)
> 3 ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK)
> 4 VEGA 36 (SANGER UK)
> 5 MSD PROTOTYPE (EBI UK)
> 6 ENSEMBL BACTERIA 3 (EBI UK)
> 7 ENSEMBL FUNGAL 3 (EBI UK)
> 8 ENSEMBL METAZOA 3 (EBI UK)
> 9 ENSEMBL PLANT 3 (EBI UK)
> ...
> > mart = useMart("plant_mart_3")
> > listDatasets(mart)
> dataset description
> 1 sbicolor_eg_gene Sorghum bicolor genes (Sbi1)
> 2 bdistachyon_eg_gene Brachypodium distachyon genes (Brachy1.0)
> 3 alyrata_eg_gene Arabidopsis lyrata genes (Araly1)
> 4 oindica_eg_gene Oryza sativa indica group genes (2005-01-BGI)
> 5 ptrichocarpa_eg_gene Populus trichocarpa genes (2004-12-JGI)
> 6 vvinifera_eg_gene Vitis vinifera genes (2007-12-IGGP)
> 7 athaliana_eg_gene Arabidopsis thaliana genes (TAIR9)
> ...
> > arabdset<-useMart(biomart="plant_mart_3", dataset = "athaliana_eg_gene")
> Checking attributes ... ok
> Checking filters ... ok
> > TSSArabAnno<-getAnnotation(arabdset, featureType="TSS")
> Error: segfault from C stack overflow
>
>
> > sessionInfo()
> R version 2.11.0 Under development (unstable) (2010-02-06 r51106)
> x86_64-unknown-linux-gnu
>
> 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_1.3.0 org.Hs.eg.db_2.3.6
> [3] GO.db_2.3.5 RSQLite_0.8-2
> [5] DBI_0.2-5 AnnotationDbi_1.9.4
> [7] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.15.4
> [9] Biostrings_2.15.20 IRanges_1.5.40
> [11] multtest_2.3.0 Biobase_2.7.4
> [13] biomaRt_2.3.1
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-5 RCurl_1.3-1 splines_2.11.0 survival_2.35-8
> [5] tools_2.11.0 XML_2.6-0
> >
>
>
> Thanks,
> P. Terry
> [email protected]
>
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>
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