cem_overlap {CEMiTool} | R Documentation

## Integrates CEMiTool analyses

### Description

Returns the occurrence of edges between different analyses

### Usage

    cem_overlap(..., analyses_list = NULL, fraction = 1)

### Arguments

`...` | Objects of class `CEMiTool`, data.frames or character string containing the path to a file with genes and modules.
`analyses_list` | List of objects of class `CEMiTool`, data.frames or character strings containing the path to files with genes and modules.
`fraction` | The fraction of objects in which an edge pair must be present to be selected (default = 1, accepts values from 0-1)

### Details

The method assumes that all genes inside each module are connected to every other gene from the same module.

### 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 cemitool twice on expr dataset. In each time, one sample will be removed
    data(expr)
    set.seed(10)
    dset1 <- expr[,-sample(1:ncol(expr), 1)]
    dset2 <- expr[,-sample(1:ncol(expr), 1)]
    cem1 <- cemitool(dset1)
    cem2 <- cemitool(dset2)
    cemoverlap_df <- cem_overlap(cem1, cem2)
    # Can also be run with a list: cemoverlap_df <- cemoverlap(list(cem1, cem2))

    # Different types of objects can be combined as well, and invalid objects will
    be removed, with a warning
    cemoverlap_df <- cem_overlap(cem1, cem2, module_genes(cem), NA, 1, NULL)

    ## End(Not run)

[Package CEMiTool version 1.0.3 Index]