Question: rtracklayer::export empty score
0
gravatar for dinocolmillo
15 days ago by
dinocolmillo0 wrote:

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 • 45 views
ADD COMMENTlink modified 15 days ago by Michael Lawrence11k • written 15 days ago by dinocolmillo0
Answer: rtracklayer::export empty score
1
gravatar for Michael Lawrence
15 days ago by
United States
Michael Lawrence11k wrote:

The score column needs to be named "score".

ADD COMMENTlink written 15 days ago by Michael Lawrence11k

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/

ADD REPLYlink written 14 days ago by dinocolmillo0
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