runLISTO: Assess the overlap of two or three lists of objects.

In LISTO: Performing Comprehensive Overlap Assessments

Assess the overlap of two or three lists of objects.

Description

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

Usage

runLISTO(
  list1,
  list2,
  list3 = NULL,
  universe1,
  universe2 = NULL,
  numCol = NULL,
  isHighTop = TRUE,
  maxCutoffs = 5000,
  mtMethod = c("BY", "holm", "hochberg", "hommel", "bonferroni", "BH", "fdr", "none"),
  pvalThr = NULL,
  nCores = 1,
  verbose = TRUE,
  ...
)

Arguments

list1	A list containing character vectors, or data frames having a numeric column.
list2	A list containing character vectors, or data frames having a numeric column.
list3	A list containing character vectors, or data frames having a numeric column.
universe1	Character vector; the set from which the items corresponding to the elements in list1 are selected.
universe2	Character vector; the set from which the items corresponding to the elements in list2 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.
pvalThr	Threshold to filter the results based on the adjusted p-values. If NULL as default, no filtering will be performed.
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).
verbose	Logical; whether the output should be verbose.
...	Additional arguments passed to mtCorrectDF.

Value

A data frame listing the p-value and adjusted p-value for each overlap. Combinations of overlaps are represented through the first two (or three if list3 is not NULL) columns, while the penultimate column records the overlap p-values and the last column records the adjusted overlap p-values.

Examples

donorPath <- system.file('extdata', 'donorMarkers.qs2', package='LISTO')
donorMarkers <- qs2::qs_read(donorPath)[seq(3)]
labelPath <- system.file('extdata', 'labelMarkers.qs2', package='LISTO')
labelMarkers <- qs2::qs_read(labelPath)[seq(3)]
universe1Path <- system.file('extdata', 'universe1.qs2', package='LISTO')
universe1 <- qs2::qs_read(universe1Path)
res <-  runLISTO(donorMarkers, labelMarkers, universe1=universe1,
numCol='avg_log2FC')

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