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]