generate.modules: Function for creation of genomic interaction modules based on...
In AQS-Group/WISH: WISH

Description Usage Arguments Value Examples

Generate.modules normalizes the epistatic interaction coefficients and performs hierarchical clustering,SNP selection and parameter selection for module construction, and generates modules. It uses the WGCNA workflow modified for epistatic correlations and outputs the module components and analysis parameters.

1 2	generate.modules(correlations,values="Coefficients",power=c(seq(1,10,0.1),c(12:22)), n.snps=dim(correlations$Coefficients)[1],minClusterSize=50,type="unsigned",threads=1)

`correlations`	List of epistatic correlations and p-values generated by epistatic.correlation()
`values`	Character which can be "Pvalues" or "Coefficients" Indicating if P-values or Coefficients should be used for analysis. The recomended and defualt values is Coefficients
`power`	Powers to test for creating scale free network. Only change if the default values don't work
`n.snps`	Number of SNPs to select. SNPs are selected by connectivity, so 500 will select the top 500 most connected Snps. Default is to use all
`minClusterSize`	Minimum module (cluster) size. Default, is 50, but changing this may be recommended in case of sparse SNPs
`type`	Type of network to generate. Default is "unsigned", can be "signed" or "signed hybrid"
`threads`	Number of threads to use if parallelization is possible.