grandR (version 0.2.7)

Wilcoxon: 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
)

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)

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?

See Also

LFC,GetContrasts