sw.perm.test(cgh) | R Documentation |
Perform a permutation test of island scores from the Smith-Waterman algorithm.
sw.perm.test(x, max.nIslands = 1, nIter = 1000, seed = NULL, trace = FALSE)
x |
a vector of real values |
max.nIslands |
number of iterations of the algorithm, each iteration finding the next highest-scoring 'island' of positive values, or NULL to find all islands |
nIter |
number of permutations of the input data used in the test |
seed |
seed for the random number generator, or NULL to use a faster random number generator that cannot be seeded |
trace |
print verbose output if TRUE |
A vector of probability values, calculated as the proportion of instances for which performing the Smith-Waterman algorithm on random permutations of the data identifies a higher-scoring island than the islands identified when the algorithm is performed on the original data
T.S.Price
## simluate vector of logratios set.seed(3) logratio <- c(rnorm(20) - 1, rnorm(20)) ## invert sign of values and subtract threshold to ensure negative mean x <- sw.threshold(logratio, function(x) median(x) + .2 * mad(x), -1) ## perform Smith-Waterman sw(x) ## perform permutation test on the islands identified sw.perm.test(x, max.nIslands = NULL, nIter= 1e4)