Query_Prep {GmicR} | R Documentation |
Query Prep
Query_Prep( Auto_WGCNA_OUTPUT, numGenes = 500, Find_hubs = FALSE, calculate_intramodularConnectivity = TRUE )
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. |
a data.frame detailing the gene symbols for each module. Gene intramodularConnectivity may also be returned. If detected, hub genes are annotated.
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)