getPImatrix {safe}R Documentation

Generation of a Pi matrix

Description

A function to generate random permutations of the data. Permutations are stored as a matrix with each row containing the permuted order as the reordered integers from 1 to n.

Usage

getPImatrix(n, K= ,method=)
getPImatrix(y.vec= , K=)
getPImatrix(block.vec=, K=)

Arguments

n Number of samples or length of the response vector
y.vec Response vector for a SAFE analysis
block.vec A character or numeric vector containing the blocking assignments (see Details:).
K Number of permutations to generate
method For method = "random" each permutation is a random reordering of 1 through n (with or without blocks). Future versions will allow method = "exaust" to give all unique permuations for a moderate number of arrays.

Details

getPImatrix is provided as a separate function from safe, so that a matrix of permutation assignments can be created and stored to reproduce identical results. In some experimental designs it may be appropriate to generate blocked permutaions of the samples, that hold another effect constant. By specifying block.vec, only the column numbers sharing a unique value in the vector will be permuted.

Value

A matrix is returned with each row containing a permutation of the integers from 1 to n. The first row is restricted to the ordered integers to represent the observed data.

Author(s)

William T. Barry: wbarry@bios.unc.edu

References

W. T. Barry, A. B. Nobel and F.A. Wright, 2004, Significance Analysis of functional categories in gene expression studies: a structured permutation approach, Bioinformatics In press.

See also the vignette included with this package.

See Also

{safe.}

Examples

## Random permutations for 8 samples
getPImatrix( n = 8, K = 5)

## Random permutations within blocks 
block <- rep(0:1,each=4)
block

getPImatrix(block.vec = block, K = 5)

[Package safe version 1.2.0 Index]