Yuchun, Thanks so much for reporting the bug, introduced recently for speedup the function! I have fixed it and committed the changes to version ChIPpeakAnno_2.12.2. It should become available at http://www.biocondu ctor.org/packages/release/bioc/html/ChIPpeakAnno.html in the next day or so. If you want to get it right away, please use svn. svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/m adman/Rpacks/ChIPpeakAnno/ Please do not hesitate to contact me and cc the Bioconductor list if you encounter additional problems. Best regards, Julie On 8/3/14 6:20 PM, "Yuchun Guo" <yguo@mit.edu> wrote: 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@umassmed.edu] Sent: Sunday, August 03, 2014 5:20 PM To: Yuchun Guo; Ou, Jianhong Cc: bioconductor@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@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 [[alternative HTML version deleted]]