performCoexFromFiles: Perform Coexpression From Files
In Sage-Bionetworks/SageBionetworksCoex: Gene Coexpression

Description Usage Arguments Details Value Note Author(s) References

Performs coexpression analysis on normalized expression data from a tabular input file. Creates diagnostic plots and output data files for the coexpression network and scale free regression statistics. The output files go into the specified directory or, if a directory is not specified, into the session's temporary directory.

1	performCoexFromFiles(inputFile, outputDir = NULL, imageFileType = "jpg", beta = NULL)

`inputFile`	A normalized matrix of gene expression data, given as a tab-delimited text file whose rows are genes/probes and whose columns are samples. The file has exactly one header row for sample IDs and one header column for gene/probe IDs, and is formatted in as expected for R, i.e. the first row has one fewer columns than the remaining rows. Note: R's limit on array size constrains the number of genes (rows) to 46340.
`outputDir`	The output directory for the created files, or NULL to use the session's temporary directory. Existing files in the specified directory are overwritten.
`imageFileType`	One of "jpg", "pdf", "png", "ps", not case sensitive. Default is "jpg".
`beta`	Soft thresholding exponent, typically 5-6. Setting to NULL (the default) causes the function to select the optimal beta between 1 and 12.

This function is a wrapper for performCoexpressionAnalysis() and createDiagnosticPlots. Additionally it creates tabular files for (1) the scale-free regression statistics (as produced by WGCNA::pickSoftThreshold()), and (2) the coexpression network. The latter is the 'network' file, a column-concatenation of (a) the input data, (b) the intramodular statistics (as produced by intraModularStatistics()), (c) the gene-wise standard deviation of the input data, and (d) the gene module assignments.

The file handles for the created plots.

`ScaleFree`	File handle to "Scale free" plot (P(k) vs. k) for optimum value of beta
`CorHeatmap`	File handle to heatmap of \|cc\|^beta, ordered according to dendrogram, with color-coded module membership along the margins
`GeneDendrogram`	File handle to gene dendrogram with color-coded modules and color names
`TOMHeatmap`	File handle to heatmap of TOM, rows and columns sorted by gene dendrogram
`GenePCDendrogram`	File handle to dendrogram of clusters of module representative genes
`ExpressionHeatmap`	File handle to heatmap of expression data, organized by gene and sample clusters
`PowerTable`	Scale-free regression statistics (as produced by WGCNA::pickSoftThreshold())
`Network`	The derived network, as described in the 'Details' section.
`GeneTree`	Gene dendrogram, an R object of the form returned by 'hclust'.