rtracklayer import only subset of ranges
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Entering edit mode
Jake ▴ 90
@jake-7236
Last seen 6 weeks ago
United States

Hi,

I have a number of bigBed files and I am trying to import only the ranges overlapping a specific window. The rtracklayer import vignette has an example of how to do this, but when I try to run the vignette it doesn't seem to import any ranges.


> test_path <- system.file("tests", package = "rtracklayer")
> test_bb <- file.path(test_path, "test.bb")
> 
> ## Returns ranges with all fields
> gr <- import(test_bb)
> gr
GRanges object with 10 ranges and 4 metadata columns:
       seqnames        ranges strand |        name     score signalValue
          <Rle>     <IRanges>  <Rle> | <character> <integer>   <numeric>
   [1]     chr1 237640-237790      * |           .        70          10
   [2]     chr1 521500-521650      * |           .       140          20
   [3]     chr1 565725-565875      * |           .       210          30
   [4]     chr1 565900-566050      * |           .       280          40
   [5]     chr1 566760-566910      * |           .       350          50
   [6]    chr10 119905-120055      * |           .       420          60
   [7]    chr10 122525-122675      * |           .       490          70
   [8]    chr10 173925-174075      * |           .       560          80
   [9]    chr10 179865-180015      * |           .       630          90
  [10]    chr10 180185-180335      * |           .       700         100
            peak
       <integer>
   [1]        -1
   [2]        -1
   [3]        -1
   [4]        -1
   [5]        -1
   [6]        -1
   [7]        -1
   [8]        -1
   [9]        -1
  [10]        -1
  -------
  seqinfo: 2 sequences from an unspecified genome
> 
> ## Retuns ranges only for 'chr10'
> ## between 180185-180185 with all fields
> which <- GRanges(c("chr10"), IRanges(c(180185, 180185)))
> rtracklayer::import(test_bb, which = which)
GRanges object with 0 ranges and 4 metadata columns:
   seqnames    ranges strand |        name     score signalValue      peak
      <Rle> <IRanges>  <Rle> | <character> <integer>   <numeric> <integer>
  -------
  seqinfo: 2 sequences from an unspecified genome
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] rtracklayer_1.54.0   GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 
[4] IRanges_2.28.0       S4Vectors_0.32.4     BiocGenerics_0.40.0 

loaded via a namespace (and not attached):
 [1] XVector_0.34.0              zlibbioc_1.40.0            
 [3] GenomicAlignments_1.30.0    BiocParallel_1.28.3        
 [5] lattice_0.20-44             rjson_0.2.21               
 [7] tools_4.1.1                 grid_4.1.1                 
 [9] SummarizedExperiment_1.24.0 parallel_4.1.1             
[11] Biobase_2.54.0              matrixStats_0.61.0         
[13] yaml_2.3.5                  crayon_1.5.0               
[15] BiocIO_1.4.0                Matrix_1.3-4               
[17] GenomeInfoDbData_1.2.7      restfulr_0.0.13            
[19] bitops_1.0-7                RCurl_1.98-1.6             
[21] DelayedArray_0.20.0         compiler_4.1.1             
[23] MatrixGenerics_1.6.0        Biostrings_2.62.0          
[25] Rsamtools_2.10.0            XML_3.99-0.9
rtracklayer • 89 views
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Entering edit mode

Looks like it might be exclusion of the start but inclusive of stop:

>  which <- GRanges(c("chr10"), IRanges(start=180185, end=180185))
>  rtracklayer::import(test_bb, which = which)
GRanges object with 0 ranges and 4 metadata columns:
   seqnames    ranges strand |        name     score signalValue      peak
      <Rle> <IRanges>  <Rle> | <character> <integer>   <numeric> <integer>
  -------
  seqinfo: 2 sequences from an unspecified genome


>  which <- GRanges(c("chr10"), IRanges(start=180185, end=180335))
>  rtracklayer::import(test_bb, which = which)
GRanges object with 1 range and 4 metadata columns:
      seqnames        ranges strand |        name     score signalValue
         <Rle>     <IRanges>  <Rle> | <character> <integer>   <numeric>
  [1]    chr10 180185-180335      * |           .       700         100
           peak
      <integer>
  [1]        -1
  -------
  seqinfo: 2 sequences from an unspecified genome




>  which <- GRanges(c("chr10"), IRanges(start=180186, end=180186))
>  rtracklayer::import(test_bb, which = which)
GRanges object with 1 range and 4 metadata columns:
      seqnames        ranges strand |        name     score signalValue
         <Rle>     <IRanges>  <Rle> | <character> <integer>   <numeric>
  [1]    chr10 180185-180335      * |           .       700         100
           peak
      <integer>
  [1]        -1
  -------
  seqinfo: 2 sequences from an unspecified genome


>  which <- GRanges(c("chr10"), IRanges(start=180335, end=180335))
>  rtracklayer::import(test_bb, which = which)
GRanges object with 1 range and 4 metadata columns:
      seqnames        ranges strand |        name     score signalValue
         <Rle>     <IRanges>  <Rle> | <character> <integer>   <numeric>
  [1]    chr10 180185-180335      * |           .       700         100
           peak
      <integer>
  [1]        -1
  -------
  seqinfo: 2 sequences from an unspecified genome
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