WGCNA_saveModuleAndMe: Save gene-module relationships, MEs and plot module...

In Tong-Chen/YSX: For Yishengxin Training

Description

Save gene-module relationships, MEs and plot module correlations.

Usage

WGCNA_saveModuleAndMe(net, datExpr, prefix = "ehbio", saveplot = NULL, ...)

Arguments

net	WGCNA_coexprNetwork or blockwiseModules returned WGCNA object.
datExpr	Expression data. A matrix (preferred) or data frame in which columns are genes and rows ar samples. NAs are allowed, but not too many. See checkMissingData below and details.
prefix	prefix for output files.
saveplot	Save plot to given file "a.pdf", "b.png".
...	Additional parameters given to plot output (pdf, png,...) like "width", "height", .etc.

Examples

df = generateAbundanceDF(nSample=30, nGrp=3, sd=5)
datExpr <- WGCNA_dataFilter(df)
datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr)
power <- WGCNA_softpower(datExpr)
net <- WGCNA_coexprNetwork(datExpr, power)
WGCNA_saveModuleAndMe(net, datExpr)

#2
exprMat <- "test.file"
wgcnaL <- WGCNA_readindata(exprMat)

traitData <- 'trait.file'
wgcnaL <- WGCNA_readindata(exprMat, traitData)
datExpr <- wgcnaL$datExpr
WGCNA_dataCheck(datExpr)
datExpr <- WGCNA_dataFilter(datExpr)
datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr)
# datExpr <- WGCNA_sampleClusterDetectOutlier(datExpr, traitColors=wgcnaL$traitColors)
power <- WGCNA_softpower(datExpr)
net <- WGCNA_coexprNetwork(datExpr, power)
MEs_col <- WGCNA_saveModuleAndMe(net, datExpr)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.