testCoAccessibilityChromVar: 'testCoAccessibilityChromVar'

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

testCoAccessibilityChromVar

Description

'r lifecycle::badge("deprecated")' This function is deprecated due as we no longer recommend using a chromVAR background set. testCoAccessibilityChromVar takes an input set of tile pairs and tests whether they are significantly different compared to a background set found via ChromVAR

Usage

testCoAccessibilityChromVar(
  SampleTileObj,
  tile1,
  tile2,
  numCores = 1,
  ZI = TRUE,
  backNumber = 1000,
  returnBackGround = FALSE,
  highMem = 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 ChromVAR-matched background pairs. Default is 1000.
returnBackGround	Boolean, if TRUE return the background correlations as well as foreground. Default is FALSE.
highMem	Boolean to control memory usage. Default is FALSE. Only set highMem to TRUE if you have plenty of memory and want to run this function faster.s
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.