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

Description

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

Usage

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

Arguments

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.

Value

vector of nucleotide positions included in the transcript

Author(s)

Wolfgang Huber, in the davidTiling R package (LGPL license)

See Also

gffRead for creating a data frame from a GTF/GFF file, and http://useast.ensembl.org/info/website/upload/gff.html for specifics of the GFF/GTF file format.

Examples

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

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