cem_overlap {CEMiTool} | R Documentation

## Integrates CEMiTool analyses

### Description

Returns the occurrence of edges between different analyses

### Usage

    cem_overlap(analyses, num_studies = 0, desired_table = "adjacency",
      verbose = TRUE)

### Arguments

`analyses` | List of objects of class `CEMiTool`
`num_studies` | The minimum number of objects in the `analyses` list in which an edge pair must be present to be selected (default = 0)
`desired_table` | Character string indicating the type of output to be returned. Default: 'adjacency'.
`verbose` | Logical. If `TRUE`, reports analysis steps.

### Details

The method assumes that all genes inside each module are connected to every other gene from the same module. Argument desired_table must be one of `spearman` (returns Spearman's rho), `pearson` (Pearson's R), `b_correlations` (returns adjacency list defined in CEMiTool object), `adjacency` (returns discretized edges)

### Value

Object of class `data.frame` containing edgelist describing common edges between the networks defined in module slots from the input objects

### Examples

    ## Not run:
    # Run the cemitool function twice on expr dataset. Each time, one sample will be removed
    data(expr0)
    set.seed(10)
    dset1 <- expr0[,-sample(1:ncol(expr0), 1)]
    dset2 <- expr0[,-sample(1:ncol(expr0), 1)]
    cem1 <- cemitool(dset1, plot=FALSE)
    cem2 <- cemitool(dset2, plot=FALSE)
    cem_overlap_df <- cem_overlap(list(cem1, cem2))

    ## End(Not run)

[Package CEMiTool version 1.6.11 Index]