testCoAccessibility {MOCHA}

testCoAccessibility

Description

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

Usage

testCoAccessibility(
  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