Dear Valerie, thank you again for your patience and the explanations. Regards, Adai On Tue, Feb 19, 2013 at 8:55 PM, Valerie Obenchain <vobencha at="" fhcrc.org=""> wrote: > Yes, evidently C1orf105 is not a 'known gene'. All Bioconductor annotations > can be found here, > > http://bioconductor.org/packages/devel/BiocViews.html#___AnnotationD ata > > The TxDb packages found on this page were made from specific tracks at UCSC > or elsewhere. The details of how a package was made can be found on the > package man page, > > ?TxDb.Hsapiens.UCSC.hg19.knownGene > > If none of the TxDb's meet your need you can create your own. In the > GenomicFeatures package there are several functions available for creating > custom annotations. > > ?makeTranscriptDbFromBiomart > ?makeTranscriptDbFromGFF > ?makeTranscriptDbFromUCSC > > I've also cc'd Marc, who handles our annotations, in case he has something > more to add. > > Valerie > > > > On 02/19/2013 10:46 AM, Adaikalavan Ramasamy wrote: >> >> Dear Valerie, >> >> Thanks once again for the quick reply. I understand there the >> different the annotation databases are not consistent and I am trying >> to understand the reason for some of the noise. If I look up >> chr1:172410869-172411762 (i.e. res[9, ]) on ucsc and also ensembl, I >> see that it overlaps with C1orf105 and PIGC >> >> >> http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr1:172410869-172 411762&hgsid=326905233&pubs=pack >> >> http://www.ensembl.org/Homo_sapiens/Location/View?r=1%3A172410869-1 72411762 >> >> so why does the GeneID is blank in this case? On the other hand res[8, >> ] calls it PIGC only. Is it because C1orf105 is not a "known gene"? >> BTW, the examples I sent were all non-intergenics. Thank you. >> >> Regards, Adai >> >> >> >> On Tue, Feb 19, 2013 at 5:21 PM, Valerie Obenchain <vobencha at="" fhcrc.org=""> >> wrote: >>> >>> Hello, >>> >>> All values in the output (GENEID, TXID, etc.) are taken from the >>> annotation >>> you are using. If the annotaion does not have a GENEID, TXID, etc. for a >>> particular range, then none will be reported. >>> >>> To take a closer look at the annotation we can extract the transcripts >>> and >>> ask for gene_id, cds_id and tx_id as columns. >>> >>> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >>> tx <- transcripts(txdb, columns=c("tx_id", "gene_id", "cds_id")) >>> >>> >>> Looking at the first 3 rows, we see none of these have a gene_id, >>> >>>>> tx[1:3] >>>> >>>> >>>> GRanges with 3 ranges and 3 metadata columns: >>>> seqnames ranges strand | tx_id >>>> gene_id >>>> <rle> <iranges> <rle> | <integer> >>>> <compressedcharacterlist> >>>> [1] chr1 [11874, 14409] + | 1 >>>> [2] chr1 [11874, 14409] + | 2 >>>> [3] chr1 [11874, 14409] + | 3 >>>> cds_id >>>> <compressedintegerlist> >>>> [1] NA >>>> [2] 1,2,3 >>>> [3] NA >>> >>> >>> >>> To isolate the portion of the annotation that overlaps with your ranges >>> you >>> can use subsetByOverlaps(), >>> >>> gr <- GRanges(c("chr1", "chr1", "chr2", "chr17", "chrX"), >>> IRanges(c(23803138, 172410967, 60890373, >>> 44061025, 153627145), width=1)) >>> res <- subsetByOverlaps(tx, gr) >>> >>> Here is an example of a transcript with no gene_id >>> >>>>> res[8:10] >>>> >>>> >>>> GRanges with 3 ranges and 3 metadata columns: >>>> seqnames ranges strand | tx_id >>>> <rle> <iranges> <rle> | <integer> >>>> [1] chr1 [172410597, 172413230] - | 6937 >>>> [2] chr1 [172410869, 172411762] - | 6938 >>>> [3] chr17 [ 43971748, 44105699] + | 59914 >>>> gene_id cds_id >>>> <compressedcharacterlist> <compressedintegerlist> >>>> [1] 5279 NA,20697 >>>> [2] 20697 >>>> [3] 4137 NA,178155,178156,... >>> >>> >>> >>> >>> Also remember that if a range is 'intergenic' that it will not have a >>> GENEID. It will have a PRECEDEID and FOLLOWID, but no GENEID. >>> >>> Valerie >>> >>> >>> >>> >>> On 02/19/2013 06:41 AM, Adaikalavan Ramasamy wrote: >>>> >>>> >>>> Dear all, >>>> >>>> I am finding some unexpected results (to me anyway) with the >>>> VariantAnnotation package. Basically, there are situations where the >>>> GENEID is missing when LOCATION is either coding, promoter, intron, >>>> threeUTR or fiveUTR. Here is an example with five SNPs (among many >>>> more). I have marked the unexpected results with "##". >>>> >>>> >>>> library(VariantAnnotation); library(TxDb.Hsapiens.UCSC.hg19.knownGene) >>>> >>>> tmp <- rbind.data.frame(c("rs10917388", "chr1", 23803138), >>>> c("rs1063412", "chr1", 172410967), >>>> c("rs78291220", "chr2", 60890373), >>>> c("rs116917239", "chr17", 44061025), >>>> c("rs11593", "chrX", 153627145) >>>> ) >>>> colnames(tmp) <- c("rsid", "chr", "pos") >>>> tmp$pos <- as.numeric( as.character(tmp$pos) ) >>>> >>>> target <- with(tmp, GRanges(seqnames = Rle(chr), >>>> ranges = IRanges(pos, >>>> end=pos, names=rsid), >>>> strand = Rle(strand("*")) >>>> ) ) >>>> >>>> loc <- locateVariants(target, TxDb.Hsapiens.UCSC.hg19.knownGene, >>>> AllVariants()) >>>> names(loc) <- NULL >>>> out <- as.data.frame(loc) >>>> out$rsid <- names(target)[ out$QUERYID ] >>>> out <- out[ , c("rsid", "seqnames", "start", "LOCATION", "GENEID", >>>> "PRECEDEID", "FOLLOWID")] >>>> out <- unique(out) >>>> rownames(out) <- NULL >>>> out >>>> >>>> rsid seqnames start LOCATION GENEID PRECEDEID >>>> FOLLOWID >>>> 1 rs10917388 chr1 23803138 intron 55616 <na> <na> >>>> 2 rs10917388 chr1 23803138 promoter <na> <na> <na> >>>> ## >>>> >>>> 3 rs1063412 chr1 172410967 intron 92346 <na> <na> >>>> 4 rs1063412 chr1 172410967 intron 5279 <na> <na> >>>> 5 rs1063412 chr1 172410967 coding 5279 <na> <na> >>>> 6 rs1063412 chr1 172410967 coding <na> <na> <na> >>>> ## >>>> >>>> 7 rs78291220 chr2 60890373 promoter <na> <na> <na> >>>> ## >>>> 8 rs78291220 chr2 60890373 intergenic <na> 64895 400957 >>>> >>>> 9 rs116917239 chr17 44061025 coding 4137 <na> <na> >>>> 10 rs116917239 chr17 44061025 intron 4137 <na> <na> >>>> 11 rs116917239 chr17 44061025 coding <na> <na> <na> >>>> ## >>>> >>>> 12 rs11593 chrX 153627145 intron 6134 <na> <na> >>>> 13 rs11593 chrX 153627145 promoter 6134 <na> <na> >>>> 14 rs11593 chrX 153627145 promoter 26778 <na> <na> >>>> 15 rs11593 chrX 153627145 promoter <na> <na> <na> >>>> ## >>>> 16 rs11593 chrX 153627145 fiveUTR <na> <na> <na> >>>> ## >>>> 17 rs11593 chrX 153627145 threeUTR <na> <na> <na> >>>> ## >>>> >>>> Can anyone help explain what is happening please? Is this to be >>>> expected? Thank you. >>>> >>>> Regards, Adai >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >