aGFF-class {ACME} | R Documentation

## Class for storing GFF-like data

### Description

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 from the Class

Objects can be created by calls of the form `new("aGFF", ...). Also, the \code{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

### Author(s)

Sean Davis

### See Also

`read.resultsGFF` and`aGFFCalc-class`

### Examples

    # Load an example
    data(example.agff)
    example.agff

[Package ACME version 1.2.1 Index]