testCoAccessibilityChromVar: `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
)

Value

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

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.