addDeviationsMatrix: Add a matrix of deviations for a given peakAnnotation to...

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

Add a matrix of deviations for a given peakAnnotation to Arrow Files in ArchRProject

Description

This function will compute peakAnnotation deviations for each ArrowFiles independently while controlling for global biases (low-memory requirement).

Usage

addDeviationsMatrix(
  ArchRProj = NULL,
  peakAnnotation = NULL,
  matches = NULL,
  bgdPeaks = getBgdPeaks(ArchRProj, method = "chromVAR"),
  matrixName = NULL,
  out = c("z", "deviations"),
  binarize = FALSE,
  version = 2,
  threads = getArchRThreads(),
  verbose = TRUE,
  parallelParam = NULL,
  force = FALSE,
  logFile = createLogFile("addDeviationsMatrix")
)

Arguments

ArchRProj	An ArchRProject object.
peakAnnotation	The name of the peakAnnotation stored in the ArchRProject.
matches	A custom peakAnnotation matches object used as input for the hypergeometric test. See motifmatchr::matchmotifs() for additional information.
bgdPeaks	A SummarizedExperiment that contains for each peak a set of background peaks matched by biases such as total accessibility and GC nucleotide content. This can be computed using addBgdPeaks and accessed by getBgdPeaks.
matrixName	The name to be used for storage of the deviations matrix in the provided ArchRProject.
out	A string or character vector that indicates whether to save the ouptut matrices as deviations ("deviations") z-scores ("z"), or both (c("deviations","z")).
binarize	A boolean value indicating whether the input matrix should be binarized before calculating deviations. This is often desired when working with insertion counts.
version	An integer for which deviations algorithm to use (1 = R native or 2 = C++ native).
threads	The number of threads to be used for parallel computing.
verbose	A boolean value that determines whether standard output includes verbose sections.
parallelParam	A list of parameters to be passed for biocparallel/batchtools parallel computing.
force	A boolean value indicating whether to force the matrix indicated by matrixName to be overwritten if it already exists in the ArrowFiles associated with the given ArchRProject.
logFile	The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Add Background Peaks
proj <- addBgdPeaks(proj, force = TRUE)

# Add Motif Deviations
proj <- addDeviationsMatrix(
  ArchRProj = proj, 
  peakAnnotation = "Motif",
  force = TRUE
)

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.