asGFF {rtracklayer} | R Documentation |
Coerce to GFF structure
Description
Coerce the structure of an object to one following GFF-like
conventions, i.e., using the Parent
GFF3 attribute to encode
the hierarchical structure. This object is then suitable for export as GFF3.
Usage
asGFF(x, ...)
## S4 method for signature 'GRangesList'
asGFF(x, parentType = "mRNA", childType = "exon")
Arguments
x |
Generally, a tabular object to structure as GFF(3) |
parentType |
The value to store in the |
childType |
The value to store in the |
... |
Arguments to pass to methods |
Value
For the GRangesList
method:
A GRanges
, with the columns: ID
(unique identifier),
Name
(from names(x)
, and the names on each element of
x
, if any), type
(as given by parentType
and
childType
), and Parent
(to relate each child range to
its parent at the top-level).
Author(s)
Michael Lawrence
Examples
## Not run:
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
exons <- exonsBy(TxDb_Hsapiens_UCSC_hg19_knownGene)
mcols(asGFF(exons))
## End(Not run)
[Package rtracklayer version 1.62.0 Index]