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?
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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