find_modules {CEMiTool} | R Documentation

## Co-expression modules definition

### Description

Defines co-expression modules

### Usage

    find_modules(cem, ...)

    ## S4 method for signature 'CEMiTool'
    find_modules(
      cem,
      cor_method = c("pearson", "spearman"),
      cor_function = "cor",
      eps = 0.1,
      set_beta = NULL,
      force_beta = FALSE,
      min_ngen = 20,
      merge_similar = TRUE,
      network_type = "unsigned",
      tom_type = "signed",
      diss_thresh = 0.8,
      verbose = FALSE
    )

### Arguments

`cem` | Object of class `CEMiTool`.
`...` | Optional parameters.
`cor_method` | A character string indicating which correlation coefficient is to be computed. Default `"pearson"`
`cor_function` | A character string indicating the correlation function to be used. Default `'cor'`.
`eps` | A value for accepted R-squared interval between subsequent beta values. Default is 0.1.
`set_beta` | A value to override the automatically selected beta value. Default is NULL.
`force_beta` | Whether or not to automatically force a beta value based on number of samples. Default is FALSE.
`min_ngen` | Minimal number of genes per submodule. Default `20`.
`merge_similar` | Logical. If `TRUE`, (the default) merge similar modules.
`network_type` | A character string indicating to use either "unsigned" (default) or "signed" networks. Default `"unsigned"`
`tom_type` | A character string indicating to use either "unsigned" or "signed" (default) TOM similarity measure.
`diss_thresh` | Module merging correlation threshold for eigengene similarity. Default `0.8`.
`verbose` | Logical. If `TRUE`, reports analysis steps. Default `FALSE`

### Value

Object of class `CEMiTool`

### Examples

    # Get example expression data
    data(expr0)
    # Initialize CEMiTool object with expression
    cem <- new_cem(expr0, filter=TRUE, apply_vst=FALSE)
    # Define network modules
    cem <- find_modules(cem)
    # Check results
    head(module_genes(cem))

[Package CEMiTool version 1.16.0 Index]