Filter detected microhaplotypes by a minimum read count

Returns a new PMO (as a raw nested list) keeping only detected microhaplotypes with reads >= read_filter. Targets with no surviving microhaplotypes, and samples with no surviving targets, are dropped. All other sections (including representative_microhaplotypes and read_counts_by_stage) are carried over unchanged.

Usage

pmo_extract_by_read_filter(pmo, read_filter)

Arguments

pmo

A PortableMicrohaplotypeObject or parsed PMO list.

read_filter

Minimum read count for a microhaplotype to be kept.

Value

A PMO list (write with write_pmo_raw()).

Examples

p <- read_pmo(
  system.file("extdata", "example_full_pmo.json.gz", package = "pmotoolsr"))
sub <- pmo_extract_by_read_filter(p, 100)