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
)fragments |
Path to tabix-indexed fragments file or a list of
|
genome |
A vector of chromosome sizes for the genome. This is used to
construct the genome bin coordinates. The can be obtained by calling
|
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 |
This function bins the genome and calls FeatureMatrix to
construct a bin x cell matrix.
Returns a sparse matrix
genome <- 780007
names(genome) <- 'chr1'
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(fpath)
GenomeBinMatrix(
fragments = fragments,
genome = genome,
binsize = 1000
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