selectGenes: Function to select genes that account for Similarity score

In MAMA: Meta-Analysis of MicroArray

Description

Genes that account for e.g 95% of Similarity score are returned.

Usage

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

Arguments

ordering	Ordered gene lists as data.frame or matrix, each column refer to one study
alpha	Selected alpha parameter for Similarity score
percent	Percentage (Numeric between 0 and 1) of the score
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

Vector of genes

Author(s)

Ivana Ihnatova

Examples

genes<-paste("Gene", 1:1000)

O<-cbind(c(sample(genes[1:200]),sample(genes[201:1000])),
         c(sample(genes[1:200]),sample(genes[201:1000])),
         c(sample(genes[1:200]),sample(genes[201:1000])) 
)
alph<-computeAlpha(100,ngenes=1000)
selectGenes(O, alph, 0.95)

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