OPPARList-class: A S4 class for the output of OPPAR main function, opa.

In DavisLaboratory/oppar: Outlier profile and pathway analysis in R

Description

A S4 class for the output of OPPAR main function, opa.

Usage

## S4 method for signature 'OPPARList'
show(object)

## S4 method for signature 'OPPARList'
x$name

Arguments

object	An object of type OPPARList
x	Object of type OPPARList.
name	Name of the slot to access.

Value

returns the number of outlier features detected, the number of samples retained, and the parameters used to run the opa function

extracts slots from an object of type OPPARList.

Methods (by generic)

• show: A show method for objects of class OPPARList

• $: A method to extract slots in OPPARList

Slots

profileMatrix

A matrix of 0, -1 and 1 representing outlier genes in samples

upper.quantile

Numeric. The upper quantile cut-off for detection of outliers

lower.quantile

Numeric. The lower quantile cut-off for detection of outliers

group

A factor vector representing the group to which each sample belong

.Data

matrix

DavisLaboratory/oppar documentation built on May 6, 2019, 1:56 p.m.