dinamic (version 1.0)

findNull: Find DiNAMIC's Null Distribution

Description

This function is used internally by DiNAMIC's detailedLook and quickLook functions. It uses the cyclic shift procedure to create an empirical distribution that provides an approximation to the distribution of max(colSums(x)) or min(colSums(x)) under the null hypothesis that no underlying CNAs are present. The empirical distribution is based on num.perms cyclic shifts of x.

Usage

findNull(x, num.perms, random.seed = NULL)

Value

A numerical vector of length num.perms.

Arguments

x

An n by m numeric matrix containing DNA copy number data from n subjects at m markers.

num.perms

A positive integer that represents the number of cyclic shifts used to create the empirical distribution.

random.seed

An optional random seed (default = NULL).

Author

Vonn Walter, Andrew B. Nobel, Fred A. Wright

Maintainer: <[e-mail]> Vonn Walter

Details

The cyclic shift procedure is detailed in Bioinformatics (2011) 27(5) 678 - 685. Briefly, cyclic shift is a permutation procedure for DNA copy number data that largely preserves the underlying correlation of the markers. This function uses num.perms cyclic shifts of the copy number matrix x to create an approximate null distribution for max(colSums(x)) or min(colSums(x)). The statistical significance of the observed value of max(colSums(x)) or min(colSums(x)) is assessed by the functions quickLook and detailedLook.

References

Walter, V., Nobel, A.B., and Wright, F.A., DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors, Bioinformatics (2011) 27(5) 678 - 685.

Examples

random.seed = 12345
set.seed(random.seed)
x = matrix(rnorm(50), 5, 10)
num.perms = 10
example.null = findNull(x, num.perms, random.seed)
#round(example.null, 2) 
#Returns 5.50 4.93 5.84 5.01 4.11 4.54 3.72 4.13 4.12 6.59