permCor {GolubRR} | R Documentation |
In Note 17 and in the caption for Figure 2, Golub et al discuss a permutation test. This function computes the relevant permutations of the data set.
permCor(exprSet, c, seed, nPerm)
exprSet |
An object of class exprSet |
c |
A vector defining two classes, the length is the same as the number of samples. |
seed |
A seed for the random number generator, so results can be reproduced. |
nPerm |
The number of permutations desired. |
For each permutation the elements of c
are rearranged and the
correlation (P
) for each gene is computed.
A list with one entry for each permutation. The element is the vector of correlations, one for each gene, with the permuted class vector.
R. Gentleman
Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring, Science, 531-537, 1999, T. R. Golub and D. K. Slonim and P. Tamayo and C. Huard and M. Gaasenbeek and J. P. Mesirov and H. Coller and M.L. Loh and J. R. Downing and M. A. Caligiuri and C. D. Bloomfield and E. S. Lander
library(golubEsets) pC1 <- permCor(golubTest[1:100,], golubTest$ALL, 1234, 10)