compute.pigengene {Pigengene} | R Documentation |
This function takes as input the expression data and module assignments, and computes an eigengene for each module using PCA.
compute.pigengene(Data, Labels, modules, saveFile = "pigengene.RData", selectedModules = "All", amplification = 5, doPlot = TRUE, verbose = 0)
Data |
A matrix or data frame containing the training expression data, with genes corresponding to columns and rows corresponding to samples. Rows and columns must be named. |
Labels |
A (preferably named) vector containing the Labels (condition types) for the training Data.
Names must agree with rows of |
modules |
A numeric vector, named by |
saveFile |
The file to save the results. |
selectedModules |
A numeric vector determining which modules to use, or set to "All" (default) to include every module. |
amplification |
An integer that controls the number of repeats for each condition.
The number of all samples roughly will be multiplied by this factor
after oversampling. See |
doPlot |
Boolean determining whether heatmaps of expression of eigengenes should be ploted and saved. |
verbose |
The integer level of verbosity. 0 means silent and higher values produce more details of computation. |
Rows of Data
are oversampled using balance
so that
each condition has roughly the same number of samples.
moduleEigengenes
computes an eigengene for each module
using PCA.
An object of pigengene-class
.
Habil Zare and Amir Foroushani
Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia, Foroushani A, Agrahari R, Docking R, Karsan A, and Zare H. In preparation.
Pigengene-package
,
one.step.pigengene
, wgcna.one.step
,
make.decision.tree
, moduleEigengenes
,
WGCNA-package
## Data: data(aml) data(mds) data(eigengenes33) d1 <- rbind(aml,mds) Labels <- c(rep("AML",nrow(aml)),rep("MDS",nrow(mds))) names(Labels) <- rownames(d1) modules33 <- eigengenes33$modules[colnames(d1)] ## Computing: pigengene <- compute.pigengene(Data=d1, Labels=Labels, modules=modules33, saveFile="pigengene.RData", doPlot=TRUE, verbose=3) class(pigengene) plot(pigengene, fontsize=12)