Hello BioC, I have a problem using refLocsToLocalLocs, predictCoding in some GRanges... rm(list=ls()) #cleaning up library(VariantAnnotation) library(BSgenome.Hsapiens.UCSC.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene roi1 <- GRanges("chr11", IRanges(108236190, width=1)) #There is roi2 <- GRanges("chr11", IRanges(108093559, width=1)) #There isn't!!! refLocsToLocalLocs(roi1, txdb) refLocsToLocalLocs(roi2, txdb) #but the position chr11:108093559 is presents in the ATM gene select(txdb, keys = 472, cols = c("TXCHROM", "TXSTRAND", "TXSTART", "TXEND", "TXID", "TXNAME"), keytype = "GENEID") #other positions with the same "empty results"... chr4:1807922, chr14:105246407, chr11:108123531 Thank you in advance for help! Ciao, Marco P.s. My sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C [5] LC_TIME=Italian_Italy.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.4.6 Rsamtools_1.10.2 TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 [4] GenomicFeatures_1.10.1 AnnotationDbi_1.20.3 Biobase_2.18.0 [7] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.26.1 Biostrings_2.26.2 [10] GenomicRanges_1.10.5 IRanges_1.16.4 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] biomaRt_2.14.0 bitops_1.0-5 DBI_0.2-5 parallel_2.15.2 RCurl_1.95-3 RSQLite_0.11.2 rtracklayer_1.18.2 stats4_2.15.2 [9] tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0

Hi Marco, On 01/07/2013 10:43 AM, Marco Lo Iacono wrote: > Hello BioC, > I have a problem using refLocsToLocalLocs, predictCoding in some GRanges... > > rm(list=ls()) #cleaning up > library(VariantAnnotation) > library(BSgenome.Hsapiens.UCSC.hg19) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > roi1 <- GRanges("chr11", IRanges(108236190, width=1)) #There is > roi2 <- GRanges("chr11", IRanges(108093559, width=1)) #There isn't!!! > refLocsToLocalLocs(roi1, txdb) > refLocsToLocalLocs(roi2, txdb) > > #but the position chr11:108093559 is presents in the ATM gene > select(txdb, keys = 472, cols = c("TXCHROM", "TXSTRAND", "TXSTART", > "TXEND", > "TXID", "TXNAME"), keytype = "GENEID") > > #other positions with the same "empty results"... > chr4:1807922, chr14:105246407, chr11:108123531 predictCoding() returns results for ranges that fall in coding regions. To see if your range is in a coding region you can use locateVariants(). > loc <- locateVariants(roi2, txdb, region=AllVariants()) >> loc > GRanges with 8 ranges and 7 metadata columns: > seqnames ranges strand | LOCATION QUERYID TXID > <rle> <iranges> <rle> | <factor> <integer> <integer> > [1] chr11 [108093559, 108093559] * | fiveUTR 1 41703 > [2] chr11 [108093559, 108093559] * | threeUTR 1 41703 > [3] chr11 [108093559, 108093559] * | promoter 1 41703 > [4] chr11 [108093559, 108093559] * | fiveUTR 1 41704 > [5] chr11 [108093559, 108093559] * | threeUTR 1 41704 > [6] chr11 [108093559, 108093559] * | promoter 1 41704 > [7] chr11 [108093559, 108093559] * | promoter 1 41705 > [8] chr11 [108093559, 108093559] * | promoter 1 43960 > CDSID GENEID PRECEDEID FOLLOWID > <integer> <character> <character> <character> > [1] <na> 472 <na> <na> > [2] <na> 472 <na> <na> > [3] <na> 472 <na> <na> > [4] <na> 472 <na> <na> > [5] <na> 472 <na> <na> > [6] <na> 472 <na> <na> > [7] <na> 472 <na> <na> > [8] <na> 4863 <na> <na> roi2 overlaps 4 different transcripts (TXID) in 2 genes (GENEID). It does not fall in a coding region but instead in UTR and promoter regions (LOCATION). So, it makes sense that you would not see predictCoding() results for this range. Valerie > > > > Thank you in advance for help! > > Ciao, Marco > > P.s. My sessionInfo() > > R version 2.15.2 (2012-10-26) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 > LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C > [5] LC_TIME=Italian_Italy.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] VariantAnnotation_1.4.6 Rsamtools_1.10.2 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 > [4] GenomicFeatures_1.10.1 AnnotationDbi_1.20.3 > Biobase_2.18.0 > [7] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.26.1 > Biostrings_2.26.2 > [10] GenomicRanges_1.10.5 IRanges_1.16.4 > BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.14.0 bitops_1.0-5 DBI_0.2-5 > parallel_2.15.2 RCurl_1.95-3 RSQLite_0.11.2 rtracklayer_1.18.2 > stats4_2.15.2 > [9] tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0 > > _______________________________________________ > 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