wgcna.one.step: Module identification
In Pigengene: Infers biological signatures from gene expression data

Description Usage Arguments Details Value References See Also Examples

This function is a wrapper function for blockwiseModules and passes its arguments to it. Some other arguments are fixed.

1 2	wgcna.one.step(Data, power, saveDir=".", blockSize = "All", saveTOMs = FALSE, doThreads=FALSE, verbose = 0, seed = NULL)

`Data`	A matrix or data frame containing the expression data, with genes corresponding to columns and rows corresponding to samples. Rows and columns must be named.
`power`	Soft-thresholding power for network construction
`saveDir`	The directory to save the results and plots. `NULL` will disable saving.
`blockSize`	The size of block when the data is too big. If not "All" (default) may introduce artifacts.
`saveTOMs`	Boolean determining if the TOM data should be saved, which can be hundreds of MBs and useful for identifying hubs.
`doThreads`	Boolean. Allows WGCNA to run a little faster using multi-threading but might not work on all systems.
`verbose`	The integer level of verbosity. 0 means silent and higher values produce more details of computation.
`seed`	Random seed to ensure reproducibility.

Data, power, blockSize, saveTOMs, verbose, and seed are passd to blockwiseModules.

A list with following components

`call`	The command that created the results
`genes`	The names of `Data` columns
`modules`	A numeric vector, named by `genes`, that reports the module (clustering) assignments.
`moduleColors`	A character vector, named by `genes`, that reports the color of each gene according to its module assignment
`net`	The full output of `blockwiseModules` function
`netFile`	The file in which the net object is saved
`power`	An echo of the `power` argument.

Langfelder P and Horvath S, WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008, 9:559

blockwiseModules, pickSoftThreshold, calculate.beta

     data(aml)
     data(mds)
     wgRes <- wgcna.one.step(Data=aml[,1:200], seed=1, power=7,
                                 saveDir="wgcna", verbose=1)