This function is used internally by DiNAMIC's
quickLook functions. It uses the cyclic shift procedure to create an empirical distribution that provides an
approximation to the distribution of
min(colSums(x)) under the null hypothesis that no underlying CNAs are present. The empirical distribution is based on
num.perms cyclic shifts of
An n by m numeric matrix containing DNA copy number data from n subjects at m markers.
A positive integer that represents the number of cyclic shifts used to create the empirical distribution.
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
min(colSums(x)). The statistical significance of the observed value of
min(colSums(x)) is assessed by the functions
A numerical vector of length num.perms.
Vonn Walter, Andrew B. Nobel, Fred A. Wright
Maintainer: <firstname.lastname@example.org> 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.
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