Test input tile pairs against a random background
Source:R/testCoAccessibility.R
testCoAccessibilityRandom.Rd`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.