do_wilcoxon {hipathia} | R Documentation

## 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")

[Package hipathia version 2.0.0 Index]