pigengene-class {Pigengene} | R Documentation

## The pigengene class

### Description

A pigengene object holds the eigengenes, weights (memberships) and other related information.

### Details

A object of class `pigengene` is the output of `compute.pigengene` function. It is a list containing at least the following components:

- `call` The call that created the results.

- `Reptimes` A named vector reporting the number of repeats for each condition in the oversampling process, which is done by the `balance` function.

- `eigenResults` The full output of `moduleEigengenes` function.

- `Data` The data matrix of gene expression.

- `Labels` A character vector giving the condition (type) for each sample (row of `Data`).

- `eigengenes` The matrix of eigengenes ordered based on `selectedModules` if provided.

- `membership` The matrix of weights of genes (rows) in all modules (columns).

- `orderedModules` The module assignment numeric vector named with genes and ordered based on module number.

- `annotation` A data frame containing labeling information useful in plotting. It has one column named "Condition". Rows have sample names.

- `saveFile` The file where the `pigengene` object is saved.

- `weightsCsvFile` The file containing the weights in csv format.

For 2 or more groups (conditions), additional (optional) components include:

- `pvalues` A numeric matrix with columns "pValue", "FDR", and "Bonferroni". Rows correspond to modules. The null hypothesis is that the eigengene is expressed with the same distribution in all groups (conditions).

- `log.pvalues` A data frame with 1 column containing the logarithm of Bonferroni-adjusted pvalues in base 10.

### See Also

`Pigengene-package`, `plot.pigengene`, `wgcna.one.step`, `compute.pigengene`, `learn.bn`, `make.decision.tree`

[Package Pigengene version 1.6.0 Index]