cyclicShiftColR: Perform the cyclic shift procedure on the columns of a matrix

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

Perform the cyclic shift procedure on the columns of a matrix

Description

Perform the cyclic shift procedure on the columns of a matrix

Usage

cyclicShiftColR(X, randomSeed = NULL)

Arguments

X	a matrix or a data frame of copy number data. The rows and columns of X correspond to genes and subjects, respectively.
randomSeed	a random seed. Default = NULL.

Details

Many algorithms for identifying recurrent DNA copy number alterations, e.g., amplifications and deletions, assess statistical significance using permutation-based null distributions. Like many genomic data types, DNA copy number data has an underlying spatial correlation structure. Randomly permuting the values within a given subject ignores this structure, and this can impact type I error rates. In contrast, cyclic permutation largely preserves the local correlation structure.

Value

a matrix Z whose dimensions are the same as X. Each column of Z is obtained by perform a cyclic shift of the corresponding column of X.

Examples

test = matrix(c(1:50), 10, 5)
cyclicShiftColR(test, randomSeed = NULL)

DiNAMIC.Duo documentation built on March 7, 2023, 8:38 p.m.