Calculate ranges x cells overlap matrix

Calculate ranges x cells overlap matrix

Usage

peak_matrix(
  fragments,
  ranges,
  mode = c("insertions", "fragments", "overlaps"),
  zero_based_coords = !is(ranges, "GRanges"),
  explicit_peak_names = TRUE
)

Arguments

fragments

Input fragments object. Must have cell names and chromosome names defined

ranges

Peaks/ranges to overlap, given as GRanges, data.frame, or list. See help("genomic-ranges-like") for details on format and coordinate systems. Required attributes:

• chr, start, end: genomic position

mode

Mode for counting peak overlaps. (See "value" section for more details)

zero_based_coords

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)

explicit_peak_names

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. Note that either way, peak names will be written when the matrix is saved.

Value

Iterable matrix object with dimension ranges x cells. When saved, the column names of the output matrix will be in the format chr1:500-1000, where start and end coords are given in a 0-based coordinate system.

mode options

• "insertions": Start and end coordinates are separately overlapped with each peak

• "fragments": Like "insertions", but each fragment can contribute at most 1 count to each peak, even if both the start and end coordinates overlap

• "overlaps": Like "fragments", but an overlap is also counted if the fragment fully spans the peak even if neither the start or end falls within the peak

Note

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.