getAttributeField {ballgown} | R Documentation |
extract a specific field of the "attributes" column of a data frame created from a GTF/GFF file
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
R package (LGPL license)
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.
gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown') gffdata = gffRead(gtfPath) gffdata$transcriptID = getAttributeField(gffdata$attributes, field = "transcript_id")