Wilcoxon: Perform Wilcoxon tests for differential expression

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Perform Wilcoxon tests for differential expression

Description

Apply the wilcoxon test for comparisons defined in a contrast matrix, requires the presto package for fast computation.

Usage

Wilcoxon(
  data,
  name.prefix = get.mode.slot(data, mode.slot)$mode,
  contrasts,
  mode.slot = DefaultSlot(data),
  genes = NULL,
  verbose = FALSE
)

Arguments

data	the grandR object
name.prefix	the prefix for the new analysis name; a dot and the column names of the contrast matrix are appended; can be NULL (then only the contrast matrix names are used)
contrasts	contrast matrix that defines all pairwise comparisons, generated using GetContrasts
mode.slot	compute mode.slot to use (should be normalized values)
genes	restrict analysis to these genes; NULL means all genes
verbose	print status messages?

Value

a new grandR object including a new analysis table. The columns of the new analysis table are

"P"	the Wilcoxon test P value
"Q"	same as P but Benjamini-Hochberg multiple testing corrected
"LFC"	the log2 fold change (only with the logFC parameter set to TRUE)

See Also

LFC,GetContrasts

grandR documentation built on Jan. 14, 2026, 5:08 p.m.