pvalObjects: Assess the overlap of two or three objects

In LISTO: Performing Comprehensive Overlap Assessments

Assess the overlap of two or three objects

Description

This function assesses the overlap of two or three objects (character vectors, or data frames having a numeric column).

Usage

pvalObjects(
  obj1,
  obj2,
  obj3 = NULL,
  universe1,
  universe2 = NULL,
  numCol = NULL,
  isHighTop = TRUE,
  maxCutoffs = 5000,
  mtMethod = c("BY", "holm", "hochberg", "hommel", "bonferroni", "BH", "fdr", "none"),
  nCores = 1,
  type = c("2N", "2MN", "3N")
)

Arguments

obj1	A data frame with a numeric column, or a character vector.
obj2	A data frame with a numeric column, or a character vector.
obj3	A data frame with a numeric column, or a character vector.
universe1	The set from which the items stored in obj1 are selected.
universe2	The set from which the items stored in obj2 are selected.
numCol	The name of the numeric column used for data frame ordering.
isHighTop	Whether higher values in the numeric column correspond to top-ranked items.
maxCutoffs	Maximum number of cutoffs. If the input data frames contain more cutoffs than this value, only maxCutoffs linearly spaced cutoffs will be selected from the generated cutoff list.
mtMethod	Multiple testing correction method.
nCores	Number of cores. If performing an overlap assessment between sets belonging to the same universe, it is recommended not to use parallelization (that is, leave this parameter as 1).
type	Type of overlap assessment. Choose between: two sets belonging to the same universe ('2N'), two sets belonging to different universes ('2MN'), three sets belonging to the same universe ('3MN').

Value

A numeric value in [0, 1] representing the p-value of the overlap of the two objects.

Examples

pvalObjects(LETTERS[seq(2, 7)], LETTERS[seq(3, 19)], universe1=LETTERS)

LISTO documentation built on April 25, 2026, 5:06 p.m.