getAttributeField: extract a specific field of the "attributes" column of a data...
In alyssafrazee/polyester: Simulate RNA-seq reads

Description Usage Arguments Value Author(s) See Also Examples

extract a specific field of the "attributes" column of a data frame created from a GTF/GFF file

1	getAttributeField(x, field, attrsep = "; ")

`x`	vector representing the "attributes" column of GTF/GFF file
`field`	name of the field you want to extract from the "attributes" column
`attrsep`	separator for the fields in the attributes column. Defaults to '; ', the separator for GTF files outputted by Cufflinks.

vector of nucleotide positions included in the transcript

Wolfgang Huber, in the davidTiling package (LGPL license)

http://useast.ensembl.org/info/website/upload/gff.html, for specifics of the GFF/GTF file format.

  library(ballgown)
  gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
  gffdata = gffRead(gtfPath)
  gffdata$transcriptID = getAttributeField(gffdata$attributes, 
    field = "transcript_id")