Test input tile pairs against a ChromVAR background
Source:R/testCoAccessibility.R
testCoAccessibilityChromVar.Rd`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.