deco-class {deco} | R Documentation

## Class `"deco"`

### Description

A list R object returned by `decoNSCA` function from DECO R package.

### Objects from the Class

Objects can be created by calls of the form `new("deco", ...)`.

### Slots

`featureTable`:

  Object of class `"data.frame"`: table of results with feature statistical information about NSCA merged with RDA information contained in 'subStatFeature' table from decoRDA function results.

`NSCAcluster`:

  Object of class `"list"`: object from NSCAcluster intern R function containing information about NSCA. If 'Binary' analysis was previously set, two lists corresponding to each class are contained (Control and Case).

`incidenceMatrix`:

  Object of class `"data.frame"`: absolute frequency matrix of 'm' features by 'n' samples size that summarizes differential events per feature per sample. It is essential for Non-symmetrical correspondence analysis.

`classes`:

  Object of class `"factor"`: vector with class labels.

`pos.iter`:

  Object of class `"numeric"`: number of iterations with DE signal.

`control`:

  Object of class `"character"`: control label.

`q.val`:

  Object of class `"numeric"`: adjusted.p.value threshold to LIMMA.

`rep.thr`:

  Object of class `"numeric"`: number of minimum repeats per sample to establish a differential event threshold.

`samp.perc`:

  Object of class `"numeric"`: minimum amount of samples showing `rep.thr` number of differential events to consider one feature as relevant (non-noisy) after RDA or subsampling step.

`subsampling.call`:

  Object of class `"numeric"`: number of minimum repeats per sample to establish a differential event threshold.

`nsca.call`:

  Object of class `"numeric"`: number of minimum repeats per sample to establish a differential event threshold.

### Methods

summary

  `summary(object = "deco")`: Prints a summary of the information inside a 'deco' R object.

show

  `show(object = "deco")`: Prints the information inside a 'deco' R object.

featureTable

  `featureTable(object = "deco")`: Extract the featureTable containing all feature statistics.

NSCAcluster

  `NSCAcluster(object = "deco")`: Extract the NSCAcluster list containing all information and tables derived from decoNSCA step.

### Author(s)

Francisco Jose Campos Laborie. <fjcamlab@usal.es>

### Examples

    showClass("deco")

    showMethods("deco")

[Package deco version 1.0.0 Index]