The metadata from rowRanges is missing in the MAP function of GenomicFiles.
1
1
Entering edit mode
Qiang ▴ 70
@qiang-9580
Last seen 21 months ago

Hi all,

I want to pass metadata ref in rowRanges to the MAP function when using reduceByFile from GenomicFiles.

fls <- tempfile()
gr <- GRanges("chr1", IRanges(c(1, 10), width = 10))
gr$ref <- c("a", "b")
gf <- GenomicFiles(files=fls, rowRanges=gr)

MAP <- function(range, file, ...){
    range
}

reduceByFile(gf, MAP = MAP)
## the same output
## reduceByFile(gr, fls, MAP = MAP)

Here are the outputs:

 [[1]]
 [[1]][[1]]
 GRanges object with 1 range and 0 metadata columns:
       seqnames    ranges strand
          <Rle> <IRanges>  <Rle>
   [1]     chr1      1-10      *
   -------
   seqinfo: 1 sequence from an unspecified genome; no seqlengths

 [[1]][[2]]
 GRanges object with 1 range and 0 metadata columns:
       seqnames    ranges strand
          <Rle> <IRanges>  <Rle>
   [1]     chr1     10-19      *
   -------
   seqinfo: 1 sequence from an unspecified genome; no seqlengths

The metadata column ref is missing when passing to the MAP function. How to pass the range corresponding metadata to the MAP function?

Thanks, Qiang

> sessionInfo()
 R version 3.6.0 (2019-04-26)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: CentOS release 6.4 (Final)

 Matrix products: default
 BLAS:   /home/qhu/usr/R-3.6/lib64/R/lib/libRblas.so
 LAPACK: /home/qhu/usr/R-3.6/lib64/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    parallel  stats     graphics  grDevices utils     datasets
 [8] methods   base

 other attached packages:
  [1] GenomicFiles_1.19.0         rtracklayer_1.43.3
  [3] Rsamtools_1.99.6            Biostrings_2.51.5
  [5] XVector_0.23.2              SummarizedExperiment_1.13.0
  [7] DelayedArray_0.9.9          BiocParallel_1.17.19
  [9] matrixStats_0.54.0          Biobase_2.43.1
 [11] GenomicRanges_1.35.1        GenomeInfoDb_1.19.3
 [13] IRanges_2.17.5              S4Vectors_0.21.23
 [15] BiocGenerics_0.29.2

 loaded via a namespace (and not attached):
  [1] Rcpp_1.0.1                compiler_3.6.0
  [3] prettyunits_1.0.2         GenomicFeatures_1.35.11
  [5] bitops_1.0-6              tools_3.6.0
  [7] zlibbioc_1.29.0           progress_1.2.0
  [9] biomaRt_2.39.3            digest_0.6.18
 [11] bit_1.1-14                BSgenome_1.51.0
 [13] RSQLite_2.1.1             memoise_1.1.0
 [15] lattice_0.20-38           pkgconfig_2.0.2
 [17] rlang_0.3.4               Matrix_1.2-17
 [19] DBI_1.0.0                 GenomeInfoDbData_1.2.1
 [21] httr_1.4.0                stringr_1.4.0
 [23] hms_0.4.2                 bit64_0.9-7
 [25] grid_3.6.0                R6_2.4.0
 [27] AnnotationDbi_1.45.1      XML_3.98-1.19
 [29] magrittr_1.5              blob_1.1.1
 [31] GenomicAlignments_1.19.1  assertthat_0.2.1
 [33] stringi_1.4.3             RCurl_1.95-4.12
 [35] VariantAnnotation_1.29.25 crayon_1.3.4

GenomicFiles • 353 views
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0
Entering edit mode
@martin-morgan-1513
Last seen 8 days ago
United States

Thanks for the nice reproducible example. Internally, the method coerces the GRanges to a GRangesList, but does so in a way that does not preserve metadata. A workaround would be to do the coercion ahead of time, e.g.,

grl <- splitAsList(gr, seq_along(gr))
reduceByFile(grl, files, MAP)
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0
Entering edit mode

The workaround works. Thanks!

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