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(expr0)
set.seed(10)
dset1 <- expr0[,-sample(1:ncol(expr0), 1)]
dset2 <- expr0[,-sample(1:ncol(expr0), 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 1.4.2 Index]