Query_Prep {GmicR}R Documentation

Query Prep

Description

Query Prep

Usage

Query_Prep(
  Auto_WGCNA_OUTPUT,
  numGenes = 500,
  Find_hubs = FALSE,
  calculate_intramodularConnectivity = TRUE
)

Arguments

Auto_WGCNA_OUTPUT

R object generated by Auto_WGCNA function.

numGenes

integer indicating the number of random genes to test for hub gene detection. Default is 500.

Find_hubs

logical value. If TRUE, module hub genes will be returned. If FALSE (default), intramodularConnectivity will be returned without hub gene identification.

calculate_intramodularConnectivity

a logical value. If TRUE (default), the intramodularConnectivity will be caluculated using the intramodularConnectivity function from WGCNA. If FALSE, a table of modules and genes will be returned without intramodularConnectivity values.

Value

a data.frame detailing the gene symbols for each module. Gene intramodularConnectivity may also be returned. If detected, hub genes are annotated.

Examples

GMIC_Builder_dir<-system.file("extdata", "GMIC_Builder.Rdata", 
package = "GmicR", mustWork = TRUE)
load(GMIC_Builder_dir)
GMIC_Builder<-Query_Prep(GMIC_Builder,  Find_hubs = TRUE)
head(GMIC_Builder$Query)

[Package GmicR version 1.0.6 Index]