[BioC] Help on sapply() with GRanges

[James W. MacDonald]

Hi Prashanatha,

On Tuesday, November 26, 2013 1:00:13 PM, Prashantha Hebbar wrote:
> Hello friends,
>
> I am trying to get genome cordinate information for list of genes using sapply function. I find an error saying "
> Error in c(values, x) :  all arguments in '...' must be CompressedList objects
>
> "
>
> Following is the code I am using.
>
> library(VariantAnnotation)
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
> txg = transcriptsBy(txdb,by="gene")

z <- txg[genes]
zr <- reduce(z)
unlist(zr)

GRanges with 3 ranges and 0 metadata columns:
       seqnames               ranges strand
          <Rle>            <IRanges>  <Rle>
    47    chr17 [40023179, 40075272]      -
  4067     chr8 [56792386, 56925006]      +
  2017    chr11 [70244612, 70282690]      +
  ---
  seqlengths:
                    chr1                  chr2 ...        chrUn_gl000249
               249250621             243199373 ...                 38502

Is that what you are trying to do?

Best,

Jim



> allGeneRange <- GRanges()
> genes<-c("47","4067","2017")
> gRangeFun <- function(i){
>        geneRange <- reduce(txg[i])
>        allGeneRange<-append(allGeneRange, geneRange)
>        return(allGeneRange)
> }
> x<-sapply(genes, gRangeFun )
> print(x)
>
> I wanted to have coordination of all genes in one GRange object to process it further. when I print x following error appears. Can somebody tell me what is going wrong with sapply() usage?
>
> Here is sessionInfo()
>
>> sessionInfo() R version 2.15.2 (2012-10-26)
> Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C         [5] LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C            [9] LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C  attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base      other attached packages: [1] VariantAnnotation_1.4.12                Rsamtools_1.10.2                        [3] Biostrings_2.26.3                       TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 [5] GenomicFeatures_1.10.2                  AnnotationDbi_1.20.7                    [7] Biobase_2.18.0                          GenomicRanges_1.10.7                    [9] IRanges_1.16.6                          BiocGenerics_0.4.0                      loaded via a namespace (and not attached): [1] BSgenome_1.26.1    DBI_0.2-7          RCurl_1.95-4.1     RSQLite_0.11.4     [5] XML_3.98-1.1       biomaRt_2.14.0     bitops_1.0-5       parallel_2.15.2    [9] rtracklayer_1.18.2 stats4_2.15.2      tools_2.15.2       zlibbioc_1.4.0
>
> Regards,
> Prashantha
> 	[[alternative HTML version deleted]]
>
>
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099