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Map probes to user-defined regions

Source: R/mapping.R
map_probes_to_features.Rd

Computes probe-to-region overlaps, preserves feature metadata, and drops regions with fewer than min_probes overlapping probes.

Usage

map_probes_to_features(se, features, min_probes = 3L)

Arguments

se

A SummarizedExperiment::SummarizedExperiment with non-empty rowRanges().

features

A GenomicRanges::GRanges of regions. If names(features) is NULL or empty, IDs region_1, region_2, ... are generated.

min_probes

Integer. Regions with fewer overlapping probes are dropped. Default 3L.

Value

A data.frame with (at minimum) columns probe_id, probe_idx, region_id, region_idx, n_probes, plus any mcols(features) columns. Attributes:

  • dropped_regions : character vector of region IDs excluded.

  • min_probes : the threshold applied.

  • n_features_in : regions supplied.

  • n_features_out : regions retained.

Details

Probes that overlap multiple regions are emitted once per region (long format). Probes with no region are silently excluded from the returned mapping. Regions excluded by min_probes (including those with zero overlaps) are recorded on attr(mapping, "dropped_regions").