MAMA (version 2.2.1)

computeAlpha: Function to do compute tunning parameter alpha

Description

Function computes vector of possible alphas in Similarity of Ordered Gene List method. See Details.

Usage

computeAlpha(n = NULL, min.weight = 1e-05, ngenes)

Arguments

n

Number of genes to be considered in the comparison , if NULL a pre-defined vector is used

min.weight

Minimal weight to be counted

ngenes

Number of genes in the dataset

Value

Details

Alphas are calculated so that at certain position (n), the exponential weights reach min.weight. If one is interessted in comparing ordered gene lists up to certain position, alpha appropriate for this position can be calculated.

References

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

Examples

#using default n
A<-computeAlpha(ngenes=1000)

#or with user-selected n
A<-computeAlpha(n=seq(from=25, to=300, by= 25),ngenes=1000)