msviper-class: The msviper class

In viper: Virtual Inference of Protein-activity by Enriched Regulon analysis

Description

This class contains the results generated by the msviper function

Slots

signature:

Matrix containing the gene expression signature

regulon:

Object of class regulon

es:

List containing 6 objects:

es$es:

Named vector of class numeric containing the enrichment scores

es$nes:

Named vector of class numeric containing the normalized enrichment scores

es$nes.se:

Named vector of class numeric containing the standard error for the normalized enrichment score

es$size:

Named vector of class numeric containing the size -number of target genes- for each regulator

es$p.value:

Named vector of class numeric containing the enrichment p-values

es$nes.bt:

Matrix containing the normalized enrichment score if the msviper test is performed with bootstraps

param:

List containing 3 elements:

param$minsize:

Integer indicating the minimum allowed size for the regulons

param$adaptive.size:

Logical indicating whether the weight (likelihood) should be used for computing the regulon size

param$iterative:

Logical indicating whether a two step analysis with adaptive redundancy estimation should be performed

nullmodel:

Matrix of genes by permutations containing the NULL model signatures

ledge:

List containing the leading edge genes for each regulator. This slot is added by the ledge function

shadow:

Two columns matrix containing the gene names for the shadow pairs. The first column contain the most probble regulator and the second column the one that was identified because a shadow effect

viper documentation built on Nov. 8, 2020, 7:37 p.m.