Prashantha, Could you please send us the session information and the code snippet with the example coordinates? Thanks! Best regards, Julie On 3/9/11 3:33 AM, "Prashantha Hebbar" <prashantha.hebbar at="" yahoo.com=""> wrote: > Dear all, > > I have few issues with TSS information obtained through ChIPpeakAnno. To > catalog > TSS information pertaining to my probe sets I have used TSS.human.GRCh37 > (ensemble) build. After obtaining information, data in the columns > distanceToFeature and shorstestDistance do not exactly match with either > SwitchGear TSS prediction available through UCSC or Eponine tss prediction > available through Ensemble. > > > Here is one such example I have encountered. > To coordinate chr11:128391471-128391952, ChIPpeakAnno gave distanceToFeature > as > 65982 and shorstestDistance as 62815. The given coordinate is from > chr11:128328656-128457453 (ETS1). if we search with same coordinate in either > UCSChg19(SwitchGear) or Ensemble (Eponine), for TSS, tss situates at 128392173 > position. if we subtract 128392173-128328656=63517. This in contradiction not > matching to the ChIPpeakAnno (65982). > > Can anybody please clarify this issue? How come with same build this > difference? > > > Thanking you in anticipation. > > Regards, > Prashantha > > Manipal Life Sciences Center, > Manipal University, > Manipal, India > PIN: 576104 > Email:prashantha.hebbar at manipal.edu > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

Prashantha, I was able to reproduce the intended distances from your example. library(ChIPpeakAnno) data(TSS.human.GRCh37) myexp = RangedData(IRanges(start=c(128391471), en=c(128391952), names=c("p1")), strand=as.integer(1),space=c("11")) annotatedPeak1= annotatePeakInBatch(myexp, AnnotationData = TSS.human.GRCh37) annotatedPeak1 space ranges | peak strand feature 11 [128391471, 128391952] | p1 - ENSG00000134954 start_position end_position insideFeature distancetoFeature shortestDistance 128328656 128457453 inside 65982 62815 Here is how the distancetoFeature is calculated. Please note that this is the start position of the peak minus the TSS position (feature end if feature is on - strand and feature start if feature is on + strand). If feature is on - strand, reverse the sign of the distance. The confusion might be due to that this feature is on the - strand. > -(128391471 - 128457453) [1] 65982 Here is the shortest distance > min(abs(128391471 - 128328656), abs(128391471 - 128457453), abs(128391952 - 128328656), abs(128391952-128457453)) [1] 62815 Best regards, Julie > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.6.0 limma_3.6.9 [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 [5] RSQLite_0.9-4 DBI_0.2-5 [7] AnnotationDbi_1.12.0 BSgenome.Ecoli.NCBI.20080805_1.3.16 [9] BSgenome_1.18.2 GenomicRanges_1.2.2 [11] Biostrings_2.18.2 IRanges_1.8.8 [13] multtest_2.6.0 Biobase_2.10.0 [15] biomaRt_2.6.0 loaded via a namespace (and not attached): [1] MASS_7.3-9 RCurl_1.4-3 splines_2.12.1 survival_2.36-2 tools_2.12.1 [6] XML_3.2-0 On 3/9/11 3:33 AM, "Prashantha Hebbar" <prashantha.hebbar at="" yahoo.com=""> wrote: > Dear all, > > I have few issues with TSS information obtained through ChIPpeakAnno. To > catalog > TSS information pertaining to my probe sets I have used TSS.human.GRCh37 > (ensemble) build. After obtaining information, data in the columns > distanceToFeature and shorstestDistance do not exactly match with either > SwitchGear TSS prediction available through UCSC or Eponine tss prediction > available through Ensemble. > > > Here is one such example I have encountered. > To coordinate chr11:128391471-128391952, ChIPpeakAnno gave distanceToFeature > as > 65982 and shorstestDistance as 62815. The given coordinate is from > chr11:128328656-128457453 (ETS1). if we search with same coordinate in either > UCSChg19(SwitchGear) or Ensemble (Eponine), for TSS, tss situates at 128392173 > position. if we subtract 128392173-128328656=63517. This in contradiction not > matching to the ChIPpeakAnno (65982). > > Can anybody please clarify this issue? How come with same build this > difference? > > > Thanking you in anticipation. > > Regards, > Prashantha > > Manipal Life Sciences Center, > Manipal University, > Manipal, India > PIN: 576104 > Email:prashantha.hebbar at manipal.edu > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >