pigengene-class {Pigengene} | R Documentation |
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.
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.
Pigengene-package
, plot.pigengene
,
wgcna.one.step
, compute.pigengene
,
learn.bn
, make.decision.tree