parseGffAttributes: Parse out the gffAttributes column of a Genome\_intervals...
In genomeIntervals: Operations on genomic intervals

Description Usage Arguments Value Note See Also Examples

GFF files contain a string, with key/value pairs separated by “;”, and the key and value separated by “=”. This function parses such strings into a list of vectors with named elements.

1	parseGffAttributes(gi)

`gi`	A `Genome_intervals` object.

A list, with one element per row of gi. Each element is a character vector with named components. Names correspond to keys, and components correspond to values.

Key/value pairs which are missing the “=” symbol, or which have nothing between it and the “;” delimiter or end of line, will generate a NA value, with a warning. Any key/value “pairs” with more than one “=” cause an error.

In many cases, getGffAttribute, in this package, is easier and faster. See the function readGff3 for loading a GFF file.

# Get file path
libPath <- installed.packages()["genomeIntervals", "LibPath"]
filePath <- file.path(
                   libPath,
                   "genomeIntervals",
                   "example_files"
                   )

# Load gff and parse attributes
gff <- readGff3( file.path( filePath, "sgd_simple.gff"), isRightOpen = FALSE )
gfatt <- parseGffAttributes(gff)

head( gfatt )