Calculate ranges x cells tile overlap matrixSource:
Calculate ranges x cells tile overlap matrix
zero_based_coords = !is(ranges, "GRanges"),
explicit_tile_names = FALSE
Input fragments object
Tiled regions given as GRanges, data.frame, or list. See
help("genomic-ranges-like")for details on format and coordinate systems. Required attributes:
end: genomic position
tile_width: Size of each tile in this region in basepairs
Must be non-overlapping and sorted by (chr, start), with chromosomes ordered according to the chromosome names of
Whether to convert the ranges from a 1-based end-inclusive coordinate system to a 0-based end-exclusive coordinate system. Defaults to true for GRanges and false for other formats (see this archived UCSC blogpost)
Boolean for whether to add rownames to the output matrix in format e.g chr1:500-1000, where start and end coords are given in a 0-based coordinate system. For whole-genome Tile matrices the names will take ~5 seconds to generate and take up 400MB of memory. Note that either way, tile names will be written when the matrix is saved.
Iterable matrix object with dimension ranges x cells. When saved, the column names will be in the format chr1:500-1000, where start and end coords are given in a 0-based coordinate system.
When calculating the matrix directly from a fragments tsv, it's necessary to first call
select_chromosomes() in order to
provide the ordering of chromosomes to expect while reading the tsv.