RankProduct: Wrapper function for RankProduct method

Description

This is a wrapper function for perfoming meta-analysis using Rank Product method.

Usage

RankProduct(data, varname, num.perm = 100, logged = TRUE, na.rm = FALSE, gene.names = NULL, plot = FALSE, rand = NULL, cutoff = 0.05)

Arguments

data

MetaArray object

varname

Character String - name of one column in clinical data matrices to be used as class labels

num.perm

Number of permutations

logged

Logical - indicating whether data are on log-scale

na.rm

Logical - if FALSE (default), the NA value will not be used in computing rank. If TRUE the missing values will be replaced by the genewise mean of the non-missing values. Gene will all value missing will be assigned "NA"

gene.names

Character vector - gene names to be be attached to the estimated percentage of false prediction (pfp)

plot

Logical - if TRUE a plot of the estimated pfp verse the rank of each gene is drawn

rand

Numeric - a seed for random number generator

cutoff

Numeric - p-value for selection of significant genes

Value

Object of class RankProduct.res containing outputs from functions: RPadvance and topGene

References

Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P.(2004) Rank Products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments, FEBS Letter, 57383-92

Examples

Run this code

data(ColonData)
rp<-RankProduct(ColonData, "satelite", num.perm=10)