[BioC] Empty Granges

[Marco Lo Iacono]

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