Query_Prep {GmicR} | R Documentation

## Query Prep

### Description

Query Prep

### Usage

    Query_Prep(
      Auto_WGCNA_OUTPUT,
      numGenes = 500,
      Find_hubs = FALSE,
      nThreads = NULL,
      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.
`nThreads` | non-negative integer specifying the number of parallel threads to be used by certain parts of correlation calculations. This option only has an effect on systems on which a POSIX thread library is available (which currently includes Linux and Mac OSX, but excludes Windows). If zero, the number of online processors will be used if it can be determined dynamically, otherwise correlation calculations will use 2 threads.
`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 1.6.0 Index]