[BioC] ChIPpeakAnno for overlapping gene features
Yuchun Guo
yguo at mit.edu
Mon Aug 4 00:20:36 CEST 2014
Hi Julie,
Attached is the sample input bed files. The gene annotation is hg19 TSS.
mart<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl") # Homo
sapiens genes (GRCh37.p13)
TSS.hg19 = getAnnotation(mart, featureType="TSS")
Thank you for the suggestion. I started with select = "all" and output =
"both". But then I used select="first", output="overlapping" when I tried to
locate the problem.
Thank you!
Yuchun
From: Zhu, Lihua (Julie) [mailto:Julie.Zhu at umassmed.edu]
Sent: Sunday, August 03, 2014 5:20 PM
To: Yuchun Guo; Ou, Jianhong
Cc: bioconductor at r-project.org
Subject: Re: ChIPpeakAnno for overlapping gene features
Yuchun,
Could you please send us the sample input so that we can replicate the
error? Thanks!
BTW, I suggest set select = "all" since you are interested in selecting all
overlapping TSSs within 5kb of the ChIP peaks. In addition, if you are
interested in both nearest and overlapping TSS, please set output = "both"
without calling the function twice.
For future correspondences, could you please cc bioconductor list so that
others could benefit and contribute? Thanks!
Best regards,
Julie
On 8/3/14 4:48 PM, "Yuchun Guo" <yguo at MIT.EDU> wrote:
Hi Julie,
I am a postdoc in David Gifford's computational genomics group at MIT. I am
using your ChIPpeakAnno package for finding genes around TF binding sites. I
would like to get your help on finding genes that have TSSs within 5000bp of
the ChIP peaks.
I can run successfully on getting the nearest genes.
peaks1 = annotatePeakInBatch(peakList[,], AnnotationData=TSS.hg19,
FeatureLocForDistance="TSS", PeakLocForDistance="middle")
But, I ran the following and got an error.
peaks2 = annotatePeakInBatch(peakList[,], AnnotationData=TSS.hg19,
FeatureLocForDistance="TSS", PeakLocForDistance="middle", maxgap=5000,
select="first", output="overlapping")
Error in matrix(as.numeric(r.o[, 7:8]), ncol = 2) :
(list) object cannot be coerced to type 'double'
Did I make some mistakes on calling the annotatePeakInBatch method? Please
let me know.
Thanks,
Yuchun
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-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=en_US.UTF-8 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] parallel grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] reactome.db_1.48.0 org.Hs.eg.db_2.14.0 ChIPpeakAnno_2.12.1
[4] AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2 Biobase_2.24.0
[7] RSQLite_0.11.4 DBI_0.2-7 Biostrings_2.32.1
[10] XVector_0.4.0 IRanges_1.22.9 BiocGenerics_0.10.0
[13] biomaRt_2.20.0 VennDiagram_1.6.7
loaded via a namespace (and not attached):
[1] BatchJobs_1.3 BBmisc_1.7 BiocParallel_0.6.1
[4] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0
[7] checkmate_1.2 codetools_0.2-8 digest_0.6.4
[10] fail_1.2 foreach_1.4.2 GenomicAlignments_1.0.3
[13] GenomicFeatures_1.16.2 GenomicRanges_1.16.3 GO.db_2.14.0
[16] iterators_1.0.7 limma_3.20.8 MASS_7.3-33
[19] multtest_2.20.0 Rcpp_0.11.0 RCurl_1.95-4.1
[22] Rsamtools_1.16.1 rtracklayer_1.24.2 sendmailR_1.1-2
[25] splines_3.1.1 stats4_3.1.1 stringr_0.6.2
[28] survival_2.37-7 tools_3.1.1 XML_3.98-1.1
[31] zlibbioc_1.10.0
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