get_mods {CEMiTool} | R Documentation

## Calculate co-expression modules

### Description

This function takes a `CEMiTool` object containing an adjacency matrix together with the given network parameters, and returns the given co-expression modules.

### Usage

    get_mods(cem, ...)

    ## S4 method for signature 'CEMiTool'
    get_mods(
      cem,
      cor_function = "cor",
      cor_method = "pearson",
      tom_type = "signed",
      min_ngen = 20
    )

### Arguments

`cem` | Object of class `CEMiTool`.
`...` | Optional parameters.
`cor_function` | A character string indicating the correlation function to be used. Default `'cor'`.
`cor_method` | A character string indicating which correlation coefficient is to be computed. Default `"pearson"`.
`tom_type` | A character string indicating to use either "unsigned" or "signed" (default) TOM similarity measure.
`min_ngen` | Minimal number of genes per module (Default: 20).

### Value

Numeric labels assigning genes to modules.

### Examples

    # Get example expression data
    data(expr0)
    # Initialize new CEMiTool object with expression data
    cem <- new_cem(expr0, filter=TRUE, apply_vst=FALSE)
    # Calculate adjacency matrix with example beta value 8
    cem <- get_adj(cem, beta=8)
    # Get module labels
    mods <- get_mods(cem)

[Package CEMiTool version 1.16.0 Index]