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 1.8.0 Index]