diggit (version 1.4.0)

diggit-class: The diggit class

Description

This class stores parameters and results of the diggit algorithm

This function generates diggit class objects

Usage

diggitClass(expset = NULL, cnv = NULL, regulon = NULL, mindy = NULL, fcnv = NULL, mr = NULL, viper = NULL, aqtl = NULL, conditional = NULL)

Arguments

expset

ExpressionSet object or numeric matrix of expression data, with features in rows and samples in columns

cnv

Numeric matrix of CNV data

regulon

Regulon class object containing the transcriptional interactome

mindy

Regulon class object containing the post-translational interactome

fcnv

Vector of F-CNV p-values

mr

Vector of master regulator Z-score (NES)

viper

Numeric matrix of VIPER results

aqtl

Numeric matrix of aQTL p-values

conditional

List containing the conditional analysis results

Value

Object of class diggit

Slots

expset:

ExpressionSet object containing the gene expression data

cnv:

Matrrix containing the CNV data

regulon:

Regulon object containing the transcriptional interactome

mindy:

Regulon object containing the post-translational interactome

fcnv:

Numeric vector containing the p-values for functional CNVs

mr:

Numeric vector of normalized enrichment scores for the MARINa analysis

viper:

Numeric matrix of normalized enrichment scores for the VIPER analysis

aqtl:

Numeric matrix of association p-values for the aQTL analysis

conditional:

List containing the conditional analysis results

Details

see diggit-methods for related methods

Examples

data(gbm.expression, package="diggitdata")
data(gbm.aracne, package="diggitdata")
dobj <- diggitClass(expset=gbmExprs, regulon=gbmTFregulon)
print(dobj)