pigengene-class: The pigengene class
In Pigengene: Infers biological signatures from gene expression data

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

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 with some fixes, e.g., we change eigengenes to a matrix, and use genes as its row names. Also, varExplained is named according to modules.
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. Rows correspond to samples.
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 a 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. See dOrderByW=TRUE.
weights The weight matrix, which is also saved in csv format. It has more columns than membership but rows may be in a different order if dOrderByW=TRUE.
heavyToLow If dOrderByW=TRUE, this will be the ordering of genes according to the modules the belong to, where the genes in each module are ordered based on the absolute value of the weights in that module. Also, the genes in the csv file are in this order.

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.

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