geneDistributionSet3-class: Class '"pathVarTwoSamplesDisc"'

In jmarlab/pathVar: Methods to Find Pathways with Significantly Different Variability

Description

This is a class representation for storing the output of the pathVarTwoSamplesDisc function.

Objects from the Class

Objects are output by the function pathVarTwoSamplesDisc. Objects can also be created by calls of the form new("geneDistributionSet3", ...).

Slots

tablePway:

A "data.table" of pathway name, pathway IDs, adjusted p-value from the boot KS test, the number of genes from our dataset inside the pathway and the total number of genes inside the pathway.

NAPways:

A character object that contains the pathway names of the pathway having no genes inside the dataset.

genesInPway1:

A list object that contains the genes from the dataset belonging to each pathway in the first group.

genesInPway2:

A list object that contains the genes from the dataset belonging to each pathway in the second group.

pwayCounts1:

A list object that contains tables of the number of genes in each cluster per pathway for the first group

pwayCounts2:

A list object that contains tables of the number of genes in each cluster per pathway for the second group

groups:

A factor object that contains the groups in which group each sample belongs to.

groupNames:

A character object that contains the names of the two groups.

var1:

A numeric object that contains the statistics (sd, mad, cv or mean) for each gene for group 1.

var2:

A numeric object that contains the statistics (sd, mad, cv or mean) for each gene for group 2.

varStat:

A character object that contains the statistics sd, mad, cv or mean chosen for the analysis.

Methods

No methods defined with class "geneDistributionSet3" in the signature.

Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

Examples

out <- new("geneDistributionSet3",tablePway=data.table::data.table(),NAPways=character(),genesInPway1=list(),genesInPway2=list(),pwayCounts1=list(),pwayCounts2=list(),groups=as.factor(c(rep(1,10),rep(2,10))),groupNames=character(),var1=c(0),var2=c(0),varStat=character())
showClass("geneDistributionSet3")

jmarlab/pathVar documentation built on May 23, 2019, 9:02 p.m.