rliger (version 1.0.0)

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)

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'.

Value

A 10-columns data.frame with test results.

Examples

# NOT RUN {
# ligerex (liger object based on in-memory datasets), factorization complete
wilcox.results <- runWilcoxon(ligerex, compare.method = "cluster")
wilcox.results <- runWilcoxon(ligerex, compare.method = "datastes", data.use = c(1, 2))
# HDF5 input
# ligerex (liger object based on datasets in HDF5 format), factorization complete
# Need to sample cells before implementing Wilcoxon test
ligerex <- readSubset(ligerex, slot.use = "norm.data", max.cells = 1000)
de_genes <- runWilcoxon(ligerex, compare.method = "clusters")
# }