geneDistributionSet-class: Class '"geneDistributionSet"'

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

Description

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

Objects from the Class

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

Slots

tablePway:

A "data.table" of pathway name, pathway IDs, adjusted p-value from the chisq test or exact 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 less than 10 genes for the Chi-Squared or also more than 500 genes for the exact test.

genesInPway:

A list object that contains each pathway with the genes from the datasets belonging to it and in which cluster they were classsify.

refProb:

A table object that contains the probability of the reference in each cluster.

refCounts:

A table object that contains the genes counts of the reference in each cluster.

pwayCounts:

A list object that contains the genes counts of the each pathway in each cluster.

numOfClus:

A numeric object that contains the number of clusters.

varStat:

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

genesInClus:

A numeric object that contains all the genes from the dataset and in which cluster they belong.

var:

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

Methods

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

Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

Examples

out <- new("geneDistributionSet",tablePway=data.table::data.table(),NAPways=character(),genesInPway=list(),refProb=table(c(1,1)),refCounts=table(c(1,1)),pwayCounts=list(),numOfClus=numeric(),varStat=character(),genesInClus=numeric(),var=numeric())
showClass("geneDistributionSet")

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