testCoAccessibilityRandom: 'testCoAccessibilityRandom'

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

testCoAccessibilityRandom

Description

'r lifecycle::badge("deprecated")' Renamed to 'testCoAccessibility' to remove unnecessary specificity around the background set, and for a shorter function name.

testCoAccessibilityRandom takes an input set of tile pairs and tests whether they are significantly different compared to random, non-overlapping background set.

Usage

testCoAccessibilityRandom(
  SampleTileObj,
  tile1,
  tile2,
  numCores = 1,
  ZI = TRUE,
  backNumber = 1000,
  calcPValue = TRUE,
  returnBackGround = FALSE,
  verbose = TRUE
)

Arguments

SampleTileObj	The SummarizedExperiment object output from getSampleTileMatrix containing your sample-tile matrices
tile1	vector of indices or tile names (chrX:100-2000) for tile pairs to test (first tile in each pair)
tile2	vector of indices or tile names (chrX:100-2000) for tile pairs to test (second tile in each pair)
numCores	Optional, the number of cores to use with multiprocessing. Default is 1.
ZI	boolean flag that enables zero-inflated (ZI) Spearman correlations to be used. Default is TRUE. If FALSE, skip zero-inflation and calculate the normal Spearman.
backNumber	number of background pairs. Default is 1000.
calcPValue	Boolean, if TRUE calculate p-values. Default is TRUE.
returnBackGround	Boolean, if TRUE return the background correlations as well as foreground. Default is FALSE.
verbose	Set TRUE to display additional messages. Default is FALSE.

Value

foreGround A data.frame with Tile1, Tile2, Correlation, and p-value for that correlation compared to the background

MOCHA documentation built on May 29, 2024, 2:25 a.m.