GenomeBinMatrix: Genome bin matrix

In timoast/signac: Analysis of Single-Cell Chromatin Data

Genome bin matrix

Description

Construct a bin x cell matrix from a fragments file.

Usage

GenomeBinMatrix(
  fragments,
  genome,
  cells = NULL,
  binsize = 5000,
  process_n = 2000,
  sep = c("-", "-"),
  verbose = TRUE
)

Arguments

fragments	Path to tabix-indexed fragments file or a list of Fragment objects
genome	A vector of chromosome sizes for the genome. This is used to construct the genome bin coordinates. The can be obtained by calling seqlengths on a BSgenome-class object.
cells	Vector of cells to include. If NULL, include all cells found in the fragments file
binsize	Size of the genome bins to use
process_n	Number of regions to load into memory at a time, per thread. Processing more regions at once can be faster but uses more memory.
sep	Vector of separators to use for genomic string. First element is used to separate chromosome and coordinates, second separator is used to separate start and end coordinates.
verbose	Display messages

Details

This function bins the genome and calls FeatureMatrix to construct a bin x cell matrix.

Value

Returns a sparse matrix

Examples

genome <- 780007
names(genome) <- 'chr1'
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(fpath)
GenomeBinMatrix(
  fragments = fragments,
  genome = genome,
  binsize = 1000
)

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.