aGFF-class {ACME} | R Documentation |
The GFF format is quite versatile while remaining simple. This class simply stores the annotation associated with a set of GFF files from the same regions of the genome along with some information about the samples from which the data came and the data (from the "score" column of the GFF file) themselves.
Objects can be created by calls of the
form new("aGFF", ...). Also, the \code{read.resultsGFF()}
function returns aGFF objects.
.
annotation
:"data.frame"
with
two columns absolutely necessary, "Chromosome" and "Location".
Other columns can be included.data
:"matrix"
of the same
number of rows as the annotation slot and the same number of
columns as the number of rows in the samples slot, containing
data for later analysissamples
:"data.frame"
for
describing the samples, one row per samplesignature(x = "aGFF")
: to plot a region along the
genome.signature(x = "aGFF")
: simple method to display
summary of aGFF objectsignature(object = "aGFF")
: simple method to display
summary of aGFF objectSean Davis
read.resultsGFF
andaGFFCalc-class
# Load an example data(example.agff) example.agff