rliger (version 1.0.1)

runWilcoxon: Perform Wilcoxon rank-sum test

Description

Perform Wilcoxon rank-sum tests on specified dataset using given method.

Usage

runWilcoxon(
  object,
  data.use = "all",
  compare.method = c("clusters", "datasets")
)

Value

A 10-columns data.frame with test results.

Arguments

object

liger object.

data.use

This selects which dataset(s) to use. (default 'all')

compare.method

This indicates the metric of the test. Either 'clusters' or 'datasets'.

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
ligerex <- optimizeALS(ligerex, k = 5, max.iters = 1)
ligerex <- quantile_norm(ligerex)
ligerex <- louvainCluster(ligerex, resolution = 0.3)
wilcox.results <- runWilcoxon(ligerex, compare.method = "clusters")
wilcox.results <- runWilcoxon(ligerex, compare.method = "datasets", data.use = c(1, 2))
if (length([e-mail]) > 0) {
    # For HDF5 based object
    # Need to sample cells and read into memory before running Wilcoxon test
    ligerex <- readSubset(ligerex, slot.use = "norm.data", max.cells = 1000)
    wilcox.results <- runWilcoxon(ligerex, compare.method = "clusters")
}