get_adj {CEMiTool} | R Documentation

## Calculate adjacency matrix

### Description

This function takes a `CEMiTool` object and returns an adjacency matrix.

### Usage

    get_adj(cem, ...)

    ## S4 method for signature 'CEMiTool'
    get_adj(cem, beta, network_type = "unsigned",
      cor_function = "cor", cor_method = "pearson")

### Arguments

`cem` | Object of class `CEMiTool`
`...` | Optional parameters.
`beta` | Selected soft-threshold value
`network_type` | A character string indicating to use either "unsigned" (default) or "signed" networks. Default `"unsigned"`.
`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"`.

### Value

Object of class `CEMiTool` with adjacency data

### 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)
    # Check results
    adj <- adj_data(cem)
    adj[1:5, 1:5]

[Package CEMiTool version 1.8.3 Index]