getCoAccessibleLinks {MOCHA}

getCoAccessibleLinks

Description

getCoAccessibleLinks takes an input set of regions (tiles) and finds co-accessible neighboring regions within a window. Co-accessibility is defined as the correlation between two region intensity (openness) across samples.

Usage

getCoAccessibleLinks(
  SampleTileObj,
  cellPopulation = "All",
  regions,
  chrChunks = 1,
  windowSize = 1 * 10^6,
  numCores = 1,
  ZI = TRUE,
  approximateTile = FALSE,
  verbose = FALSE
)

Arguments

SampleTileObj

The SummarizedExperiment object output from getSampleTileMatrix containing your sample-tile matrices

cellPopulation

A string denoting the cell population of interest, which must be present in SampleTileObj

regions

a GRanges object or vector or strings containing the regions on which to compute co-accessible links. Strings must be in the format "chr:start-end", e.g. "chr4:1300-2222". Can be the output from getDifferentialAccessibleTiles.

chrChunks

This functions subsets by groups of chromosome, and then parallelizes within each group of chromosomes when running correlations. This method keeps memory low. To speed things up on high performing platforms, you can chunk out more than one chromosome at a time. Default is chrChunks = 1, so only one chromosome at a time.

windowSize

the size of the window, in basepairs, around each input region to search for co-accessible links

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.

approximateTile

If set to TRUE, it will use all tiles that overlap with the regions given, instead of finding an exact match to the regions variable. Default is FALSE.

verbose

Set TRUE to display additional messages. Default is FALSE.

Details

The technical details of the zero-inflated correlation can be found here:

Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated Data" (2009). Dissertations.

while the implementation (scHOT R package), can be found here: http://www.bioconductor.org/packages/release/bioc/html/scHOT.html

Value

TileCorr A data.table correlation matrix