Construct explicit non-overlapping genome tiles and delegate
validated sparse fragment counting to RecountATAC(). No peaks are needed
for defining the tile universe; the source ChromatinAssay supplies verified
fragment mappings and reference provenance.
Usage
RunGenomeTiles(
object,
assay = NULL,
seqlengths = NULL,
chromosomes = NULL,
bin.size = 5000L,
cells = NULL,
new.assay = NULL,
process_n = 2000L,
max.tiles = 2000000L,
verbose = TRUE
)Arguments
- object
A Seurat object with a validated ChromatinAssay and fragments.
- assay
Source chromatin assay; NULL uses the active assay.
- seqlengths
Optional named positive integer chromosome lengths. NULL uses declared assay lengths, which must all be known for selected contigs. Supplied lengths must agree with known assay lengths. Names are not used to guess assembly or chromosome style.
- chromosomes
Optional unique contig names in desired output order.
- bin.size
Positive integer tile width. The last tile per chromosome is truncated at that chromosome's end, never dropped or extended.
- cells
Selected source-assay cells; see
RecountATAC().- new.assay
Optional unused assay name; NULL returns counts/ranges/receipt.
- process_n
FeatureMatrix chunk size; see
RecountATAC().- max.tiles
Positive integer upper bound on tile count before allocation.
- verbose
Whether to print progress messages.
Value
The RecountATAC() return value with tile parameters in its receipt.
Counts are overlapping fragment records, not insertion endpoints or unique
fragments across bins. A fragment crossing a boundary can count in two bins.