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 read.resultsGFF()
function returns aGFF objects.
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
signature(x = "aGFF")
: to plot a region along the
genome.
signature(x = "aGFF")
: simple method to display
summary of aGFF object
signature(object = "aGFF")
: simple method to display
summary of aGFF object
Sean Davis
read.resultsGFF
andaGFFCalc-class
# Load an example data(example.agff) example.agff