densityEstimate {PCpheno} | R Documentation |
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.
densityEstimate(genename,interactome,perm)
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. |
List of observed and simulated ratios.
N. LeMeur
data(ScISI) data(essglist) essential <- names(essglist) ScISI <- as.matrix(ScISI) ratio<- densityEstimate(genename=essential,interactome=ScISI,perm=50)