rtracklayer::export empty score
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Entering edit mode
@dinocolmillo-22425
Last seen 2.6 years ago

Hi, first question here

I'm trying to export a GRanges object with rtracklayer's function "export", but the gscores are all stored as 0 in the newly created file.

phast <-phastCons100way.UCSC.hg19
gs1 <- gscores(phast, GRanges(seqnames="chr22", IRanges(start=50967020:50967025, width=1)))
gs1
GRanges object with 6 ranges and 1 metadata column:
      seqnames    ranges strand |   default
         <Rle> <IRanges>  <Rle> | <numeric>
  [1]    chr22  50967020      * |         1
  [2]    chr22  50967021      * |         1
  [3]    chr22  50967022      * |       0.8
  [4]    chr22  50967023      * |         1
  [5]    chr22  50967024      * |         1
  [6]    chr22  50967025      * |         0

My GRanges object has gscores in "default", but then in the file they are at 0:

rtracklayer::export(gs1, "test.bed")

This is the content of the test.bed file:

chr22   50967019    50967020    .   0   .
chr22   50967020    50967021    .   0   .
chr22   50967021    50967022    .   0   .
chr22   50967022    50967023    .   0   .
chr22   50967023    50967024    .   0   .
chr22   50967024    50967025    .   0   .

Thanks

PD: my session info

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] rtracklayer_1.46.0              phastCons100way.UCSC.hg19_3.7.2 phastCons100way.UCSC.hg38_3.7.1
 [4] shiny_1.4.0                     GenomicScores_1.10.0            GenomicRanges_1.38.0           
 [7] GenomeInfoDb_1.22.0             IRanges_2.20.0                  S4Vectors_0.24.0               
[10] BiocGenerics_0.32.0            

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.16.0   tidyselect_0.2.5              BiocVersion_3.10.1           
 [4] purrr_0.3.3                   lattice_0.20-38               vctrs_0.2.0                  
 [7] htmltools_0.4.0               BiocFileCache_1.10.2          yaml_2.2.0                   
[10] interactiveDisplayBase_1.24.0 blob_1.2.0                    XML_3.98-1.20                
[13] rlang_0.4.1                   pillar_1.4.2                  later_1.0.0                  
[16] glue_1.3.1                    DBI_1.0.0                     BiocParallel_1.20.0          
[19] rappdirs_0.3.1                bit64_0.9-7                   dbplyr_1.4.2                 
[22] matrixStats_0.55.0            GenomeInfoDbData_1.2.2        zlibbioc_1.32.0              
[25] Biostrings_2.54.0             memoise_1.1.0                 Biobase_2.46.0               
[28] fastmap_1.0.1                 httpuv_1.5.2                  curl_4.2                     
[31] AnnotationDbi_1.48.0          Rcpp_1.0.3                    xtable_1.8-4                 
[34] backports_1.1.5               promises_1.1.0                BSgenome_1.54.0              
[37] BiocManager_1.30.10           DelayedArray_0.12.0           jsonlite_1.6                 
[40] XVector_0.26.0                mime_0.7                      bit_1.1-14                   
[43] Rsamtools_2.2.1               AnnotationHub_2.18.0          digest_0.6.22                
[46] dplyr_0.8.3                   grid_3.6.0                    tools_3.6.0                  
[49] bitops_1.0-6                  magrittr_1.5                  RCurl_1.95-4.12              
[52] tibble_2.1.3                  RSQLite_2.1.2                 crayon_1.3.4                 
[55] pkgconfig_2.0.3               zeallot_0.1.0                 Matrix_1.2-17                
[58] assertthat_0.2.1              httr_1.4.1                    R6_2.4.1                     
[61] GenomicAlignments_1.22.1      compiler_3.6.0
rtracklayer • 393 views
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Entering edit mode
@michael-lawrence-3846
Last seen 10 months ago
United States

The score column needs to be named "score".

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Entering edit mode

Thanks for your quick answer!

Since gscores() seems to return the scores under the colname of the selected population, I'm using this answer to make the export: https://www.biostars.org/p/89341/

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