MAMA (version 2.1.0)

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

• Similarity Score

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)