sigScore: Function to calculate signifficance of similarity score

In MAMA: Meta-Analysis of MicroArray

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

Signifficance of similarity score in form of p-value

Author(s)

Ivana Ihnatova

Examples

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

## End(Not run)

MAMA documentation built on Jan. 15, 2017, 3:05 p.m.