generateMatrix: generateMatrix

In plantformatics/Socrates: Analysis of scATAC-seq data

generateMatrix

Description

This function generates the sparse matrix from equally sized genomic bins or ACRs.

Usage

generateMatrix(
  obj,
  filtered = T,
  windows = 1000,
  peaks = FALSE,
  blacklist = NULL,
  organelle_scaffolds = NULL,
  verbose = T
)

Arguments

obj	Object output from findCells or buildMetaData. Required.
filtered	Logical. Whether or not to use the filtered set of cells. Defaults to TRUE.
windows	Integer. Window size to build bins. If the 'peaks' parameter is set to TRUE, this argument is over-ridden.
peaks	Logical. If TRUE, use ACRs to build sparse matrix instead of genomic tiles. Default is set to FALSE.
blacklist	in bed format. If given removes black list regions from either peaks or generated bins. Default is set to null. Default is set to FALSE.
verbose	Logical. Whether or not to print progress.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.