Entering edit mode
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@mit.edu> wrote:
Hi Julie,
I am a postdoc in David Giffords 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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