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.
Arguments
Objects from the Class
Objects can be created by calls of the
form new("aGFF", ...). Also, the read.resultsGFF()
function returns aGFF objects.
Slots
annotation:
Object of class "data.frame" with
two columns absolutely necessary, "Chromosome" and "Location".
Other columns can be included.
data:
Object of class "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 analysis
samples:
Object of class "data.frame" for
describing the samples, one row per sample
Methods
plot
signature(x = "aGFF"): to plot a region along the
genome.
print
signature(x = "aGFF"): simple method to display
summary of aGFF object
show
signature(object = "aGFF"): simple method to display
summary of aGFF object