GenomeBinMatrix function

Genome bin matrix

Construct a bin x cell matrix from a fragments file.

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

Returns

Returns a sparse matrix

Details

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