Question: problem with locateVariants
gravatar for mattia pelizzola
6.0 years ago by
mattia pelizzola200 wrote:
Hello, I am getting no matches using locateVariants, while I would expect some. Here is one example: gr= GRanges(seqnames=Rle('chr12'), ranges= IRanges(33804059, 33804059)) txdb= TxDb.Mmusculus.UCSC.mm9.knownGene length(locateVariants(query= gr, subject= txdb, region=AllVariants())) [1] 0 Warning message: In `start<-`(`*tmp*`, value = c(4795974L, 4795974L, 4845775L, 4845775L, : trimmed start values to be positive (by the way, I also do not understand what this warning message is referring to) while I would expect a match to this TxDb entry: transcripts(txdb)[10888] GRanges with 1 range and 2 metadata columns: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] chr12 [33796576, 33832451] - | 38273 uc007nil.1 --- seqlengths: chr1 chr2 chr3 ... chrY_random chrUn_random 197195432 181748087 159599783 ... 58682461 5900358 thanks for any help on this, I hope it has not been asked before, mattia sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] TxDb.Mmusculus.UCSC.mm9.knownGene_2.10.1 [2] GenomicFeatures_1.14.2 [3] AnnotationDbi_1.24.0 [4] Biobase_2.22.0 [5] VariantAnnotation_1.8.6 [6] Rsamtools_1.14.2 [7] Biostrings_2.30.1 [8] GenomicRanges_1.14.3 [9] XVector_0.2.0 [10] IRanges_1.20.6 [11] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1 RSQLite_0.11.4 [5] XML_3.95-0.2 biomaRt_2.18.0 bitops_1.0-6 rtracklayer_1.22.0 [9] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 [[alternative HTML version deleted]]
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