densityEstimate: Observed versus Expected Ratios

In PCpheno: Phenotypes and cellular organizational units

Description

Function to calculate the ratio of genes that characterize a phenotype (observed) among the genes that characterize a biological complex versus the ratio of a set of randomly sampled genes (expected) among the genes that characterize a biological complex.

Usage

densityEstimate(genename,interactome,perm)

Arguments

genename	Character vector of the gene names that characterize a specific phenotype.
interactome	Contingency matrix of genes (rows) and biological complexes (columns) (see package ScISI)
perm	Numeric vector indicating the number of simulations to run to compute the expected ratios.

Value

List of observed and simulated ratios.

Author(s)

N. LeMeur

Examples

 data(ScISI)
 data(essglist)
 essential <- names(essglist)
 ScISI <- as.matrix(ScISI)
  ratio<- densityEstimate(genename=essential,interactome=ScISI,perm=50)

PCpheno documentation built on Nov. 8, 2020, 5:10 p.m.