findNull: Find DiNAMIC's null distribution

In DiNAMIC.Duo: Finding Recurrent DNA Copy Number Alterations and Differences

Find DiNAMIC's null distribution

Description

Find DiNAMIC's null distribution

Usage

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

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).

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)) as assessed by the quickLook and detailedLook procedures described in the Bioinformatics paper.

Value

A numerical vector of length num.perms

Examples

random.seed = 12345
set.seed(random.seed)
x = matrix(rnorm(50), 5, 10)
num.perms = 10
findNull(x, num.perms, random.seed)

DiNAMIC.Duo documentation built on April 11, 2025, 6:09 p.m.