MAMA (version 2.2.1)

sigScore: Function to calculate signifficance of similarity score

Description

Function calculates empirical signifficance of similarity score by means of random permutation of ordered gene lists, computing the similarity scores and comparing them to the value observed in original ordering of the genes.

Usage

sigScore(ranking, alpha, B, min.weight = 1e-05, two.sided = TRUE)

Arguments

ranking

Ordered gene lists as data.frame or matrix, each column refer to one study

alpha

Selected alpha parameter for Similarity score

B

Number of permutation

min.weight

Minimal weight for similarity score calculation

two.sided

if TRUE both top and bottom of the ordering considered, if FALSE only top positions are considered

Value

Examples

## Not run: 
# genes<-paste("Gene", 1:100)
# O<-cbind(sample(genes), sample(genes), sample(genes))
# sigScore(O, 0.0001, 100)
# ## End(Not run)