Removing metadata rows containing NA values in GRanges
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Timucin • 0
@3a63554b
Last seen 7 weeks ago
Singapore

I'm looking for promoters for protein coding transcripts in GRanges, and I end up with lots of NA values in my protein_id metadata column. Is there a way to remove the rows corresponding to the metadata column containing NA?

> ahub <- AnnotationHub()
> query(ahub, c("GRanges","Homo sapiens","GRCh38"))
> ahub['AH28674']
> gtf <- ahub[['AH28674']]

#Create a Granges object for the promoters of all protein-coding transcripts

> gtf[,"protein_id"]
> promoters <- promoters(gtf[,"protein_id"], upstream = 1500, downstream = 500)
> promoters
GRanges object with 2661879 ranges and 1 metadata column:
            seqnames      ranges strand |  protein_id
               <Rle>   <IRanges>  <Rle> | <character>
        [1]        1 10369-12368      + |        <NA>
        [2]        1 10369-12368      + |        <NA>
        [3]        1 10369-12368      + |        <NA>
        [4]        1 11113-13112      + |        <NA>
        [5]        1 11721-13720      + |        <NA>
        ...      ...         ...    ... .         ...
  [2661875]       MT 14388-16387      + |        <NA>
  [2661876]       MT 14388-16387      + |        <NA>
  [2661877]       MT 15524-17523      - |        <NA>
  [2661878]       MT 15524-17523      - |        <NA>
  [2661879]       MT 15524-17523      - |        <NA>
  -------
  seqinfo: 270 sequences (1 circular) from GRCh38 genome
IRanges GRanges NA • 212 views
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2
Entering edit mode
ATpoint ★ 1.9k
@atpoint-13662
Last seen 1 hour ago
Germany

Something like this:

keep <- !is.na(mcols(promoters)$protein_id)
promoters[keep,]
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