Hi,

I can not find  a way to do it.

exons <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene")

unlist(exons)

# this will lost the gene name information.

How do I add the name of the gene for the exons?

I have read https://www.biostars.org/p/101513/ and A: Fast way to access metadata for GRangesList?

thanks.

Tommy

stack(exons, "gene")

Hi,

The gene ids are stored in the names of the GRangesList object:

ex_by_gene <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene,
                      by="gene")
names(ex_by_gene)[1:3]
# [1] "1"   "10"  "100"

Unlisting doesn't loose them:

exons <- unlist(ex_by_gene)
names(exons)[1:29]
#  [1] "1"   "1"   "1"   "1"   "1"   "1"   "1"   "1"   "1"   "1"   "1"   "1"  
# [13] "1"   "1"   "1"   "10"  "10"  "100" "100" "100" "100" "100" "100" "100"
# [25] "100" "100" "100" "100" "100"

To put them in a metadata column:

mcols(exons)$gene_id <- names(exons)
exons
# GRanges object with 272776 ranges and 3 metadata columns:
#        seqnames               ranges strand |   exon_id   exon_name     gene_id
#           <Rle>            <IRanges>  <Rle> | <integer> <character> <character>
#      1    chr19 [58858172, 58858395]      - |    250809        <NA>           1
#      1    chr19 [58858719, 58859006]      - |    250810        <NA>           1
#      1    chr19 [58859832, 58860494]      - |    250811        <NA>           1
#      1    chr19 [58860934, 58862017]      - |    250812        <NA>           1
#      1    chr19 [58861736, 58862017]      - |    250813        <NA>           1
#    ...      ...                  ...    ... .       ...         ...         ...
#   9997    chr22 [50961997, 50962853]      - |    266958        <NA>        9997
#   9997    chr22 [50963871, 50964033]      - |    266960        <NA>        9997
#   9997    chr22 [50963901, 50964034]      - |    266961        <NA>        9997
#   9997    chr22 [50964430, 50964570]      - |    266963        <NA>        9997
#   9997    chr22 [50964675, 50964905]      - |    266965        <NA>        9997
#   -------
#   seqinfo: 93 sequences (1 circular) from hg19 genome

Hope this helps,

H.