Find DiNAMIC's Null Distribution
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.
findNull(x, num.perms, random.seed = NULL)
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). |
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.
A numerical vector of length num.perms.
Vonn Walter, Andrew B. Nobel, Fred A. Wright
Maintainer: <vwalter@email.unc.edu> Vonn Walter
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.
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
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