automaticNetworkScreening: One-step automatic network gene screening

View source: R/Functions.R

automaticNetworkScreeningR Documentation

One-step automatic network gene screening

Description

This function performs gene screening based on a given trait and gene network properties

Usage

automaticNetworkScreening(
   datExpr, 
   y, 
   power = 6, 
   networkType = "unsigned", 
   detectCutHeight = 0.995,
   minModuleSize = min(20, ncol(as.matrix(datExpr))/2), 
   datME = NULL, 
   getQValues = TRUE, 
   ...)

Arguments

datExpr

data frame containing the expression data, columns corresponding to genes and rows to samples

y

vector containing trait values for all samples in datExpr

power

soft thresholding power used in network construction

networkType

character string specifying network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "hybrid".

detectCutHeight

cut height of the gene hierarchical clustering dendrogram. See cutreeDynamic for details.

minModuleSize

minimum module size to be used in module detection procedure.

datME

optional specification of module eigengenes. A data frame whose columns are the module eigengenes. If given, module analysis will not be performed.

getQValues

logical: should q-values (local FDR) be calculated?

...

other arguments to the module identification function blockwiseModules

Details

Network screening is a method for identifying genes that have a high gene significance and are members of important modules at the same time. If datME is given, the function calls networkScreening with the default parameters. If datME is not given, module eigengenes are first calculated using network analysis based on supplied parameters.

Value

A list with the following components:

networkScreening

a data frame containing results of the network screening procedure. See networkScreening for more details.

datME

calculated module eigengenes (or a copy of the input datME, if given).

hubGeneSignificance

hub gene significance for all calculated modules. See hubGeneSignificance.

Author(s)

Steve Horvath

See Also

networkScreening, hubGeneSignificance, networkScreening, cutreeDynamic


WGCNA documentation built on April 23, 2022, 1:06 a.m.