beams {LMGene}R Documentation

Beam search rountine for finding the optimal parameters

Description

This routine finds optimal values of the two parameters, alpha and lambda, for the glog transformation function

Usage

beams(eS, startvar)

Arguments

eS Array data. must be a exprSet type
startvar Given (initial) value of log(alpha) and lambda

Details

The input argument, eS, must be exprSet type from Biobase package. If you have a matrix data and information about the considered factors, then you can use neweS to conver the data into exprSet. Please see neweS in more detail.
eS is used only as an argument when calling msecalc in the function.

Value

bestsol A vector containing best alpha and lambda value

Author(s)

David Rocke and Geun-Cheol Lee

References

http://www.idav.ucdavis.edu/~dmrocke/

See Also

msecalc, tranest2

Examples

#library
library(Biobase)
library(LMGene)

#data
data(Smpd0)

#
mat1 <- as.matrix(Smpd0@exprs)
lamstart <- log(median(abs(mat1))^2)
alphastart <- quantile(abs(as.vector(mat1)), 0.1)
startvar <- c(lamstart, alphastart)

beams(Smpd0, startvar)

[Package LMGene version 1.0.0 Index]