MAMA (version 2.2.1)

prelimScore: Function compute preliminary Similarity Score for Ordered Gene Lists

Description

Function computes preliminary Similarity Score as defined in Yang, 2005.

Usage

prelimScore(ordering, alpha, min.weight = 1e-05, two.sided = TRUE)

Arguments

ordering

Data frame, where columns refer to ordered gene list from one study

alpha

Numeric parameter used in weights exp(-alpha*n)

min.weight

minimal weight to be counted

two.sided

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

Value

References

Yang, X., Bentink, S., Scheid, S. Spang, R., Similarities of ordered gene lists, 2005

Examples

genes<-paste("Gene", 1:100)
O<-cbind(sample(genes), sample(genes), sample(genes))
prelimScore(O, 0.1)