do_wilcoxon: Apply Wilcoxon test

In babelomics/hipathia: HiPathia: High-throughput Pathway Analysis

Apply Wilcoxon test

Description

Performs a Wilcoxon test for the values in sel_vals comparing conditions g1 and g2

Usage

do_wilcoxon(
  data,
  group,
  g1,
  g2,
  paired = FALSE,
  adjust = TRUE,
  sel_assay = 1,
  order = FALSE
)

Arguments

data	Either a SummarizedExperiment object or a matrix, containing the values. Columns represent samples.
group	Either a character indicating the name of the column in colData including the classes to compare, or a character vector with the class to which each sample belongs. Samples must be ordered as in data
g1	String, label of the first group to be compared
g2	String, label of the second group to be compared
paired	Boolean, whether the samples to be compared are paired. If TRUE, function wilcoxsign_test from package coin is used. If FALSE, function wilcox.test from package stats is used.
adjust	Boolean, whether to adjust the p.value with Benjamini-Hochberg FDR method
sel_assay	Character or integer, indicating the assay to be normalized in the SummarizedExperiment. Default is 1.
order	Boolean, whether to order the results table by the FDRp.value column. Default is FALSE.

Value

Dataframe with the result of the comparison

Examples

data(path_vals)
data(brca_design)
sample_group <- brca_design[colnames(path_vals),"group"]
comp <- do_wilcoxon(path_vals, sample_group, g1 = "Tumor", g2 = "Normal")

babelomics/hipathia documentation built on July 27, 2022, 2:23 p.m.