[BioC] Empty Granges

[Valerie Obenchain]

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
>
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