Need Help w/ Subset on GRangesList
2
0
Entering edit mode
mat149 ▴ 70
@mat149-11450
Last seen 19 hours ago
United States

Hello,

Can someone help me to subset each first intron (only) from a GRangesList representing intronsByTranscript? I've been somewhat out of practice for a period of time, and I'm stuck. Thanks,

tx

TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: GCA_007735645.1
# Organism: Venturia.effusa
# Taxonomy ID: 50376
# miRBase build ID: NA
# Genome: ASM773564v1
# Nb of transcripts: 10897
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2024-02-01 11:28:21 -0500 (Thu, 01 Feb 2024)
# GenomicFeatures version at creation time: 1.52.1
# RSQLite version at creation time: 2.3.1
# DBSCHEMAVERSION: 1.2

intr<-intronsByTranscript(tx)
intr


GRangesList object of length 10897:
$`1`
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 21 sequences from ASM773564v1 genome

$`2`
GRanges object with 1 range and 0 metadata columns:
        seqnames        ranges strand
           <Rle>     <IRanges>  <Rle>
  [1] CP042185.1 102664-102719      +
  -------
  seqinfo: 21 sequences from ASM773564v1 genome

$`3`
GRanges object with 1 range and 0 metadata columns:
        seqnames        ranges strand
           <Rle>     <IRanges>  <Rle>
  [1] CP042185.1 114417-114472      +
  -------
  seqinfo: 21 sequences from ASM773564v1 genome

...
<10894 more elements>


> intr[10400]

GRangesList object of length 1:
$`10400`
GRanges object with 2 ranges and 0 metadata columns:
        seqnames        ranges strand
           <Rle>     <IRanges>  <Rle>
  [1] CP042202.1 614609-614653      -
  [2] CP042202.1 615053-615568      -
  -------
  seqinfo: 21 sequences from ASM773564v1 genome




> la<-lapply(intr,"[[",1)

Error in getListElement(x, i, ...) : 
  GRanges objects don't support [[, as.list(), lapply(), or unlist() at the
  moment
GenomicRange GenomicRanges • 185 views
ADD COMMENT
2
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

How about this?

> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> intr <- intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene)
> unlist(intr)[names(intr)[lengths(intr) > 0L]]
GRanges object with 72404 ranges and 0 metadata columns:
              seqnames        ranges strand
                 <Rle>     <IRanges>  <Rle>
      1           chr1   12228-12612      +
      2           chr1   12228-12594      +
      3           chr1   12228-12645      +
      7           chr1 322229-324287      +
      8           chr1 324061-324287      +
    ...            ...           ...    ...
  82952 chrUn_gl000228 114116-123599      +
  82953 chrUn_gl000228   31036-31352      -
  82954 chrUn_gl000228   31036-31352      -
  82956 chrUn_gl000237     1004-2472      -
  82957 chrUn_gl000241   20482-22731      -
  -------
  seqinfo: 93 sequences (1 circular) from hg19 genome

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