geneDistributionSet-class {pathVar} | R Documentation

## Class `"geneDistributionSet"`

### 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")

[Package pathVar version 1.12.0 Index]