geneDistributionSet3-class {pathVar} | R Documentation

## Class `"pathVarTwoSamplesDisc"`

### 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")

[Package pathVar version 1.22.0 Index]