do_wilcoxon: Apply Wilcoxon test

Description Usage Arguments Value Examples

View source: R/stats.R

Description

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

Usage

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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

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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")

hipathia documentation built on Nov. 8, 2020, 7:52 p.m.