| cyclicShiftColR {DiNAMIC.Duo} | R Documentation |
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)