deco-class: Class '"deco"'

In fjcamlab/deco: Decomposing Heterogeneous Cohorts using Omic Data Profiling

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. <[e-mail]>

Examples

showClass("deco")

showMethods("deco")

fjcamlab/deco documentation built on Aug. 18, 2024, 4:28 a.m.