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Count the number of targets detected per library sample

pmo_count_targets_per_library_sample.Rd

Count the number of targets detected per library sample

Usage

pmo_count_targets_per_library_sample(pmo, min_reads = 0)

Arguments

pmo

A PortableMicrohaplotypeObject or parsed PMO list.

min_reads

Minimum summed reads for a target (across its detected microhaplotypes) for that target to be counted.

Value

A tibble with columns bioinformatics_run_id, library_sample_name, target_number. Note: bioinformatics_run_id is 1-based; when a detected set has no run id, a detected_microhaplotypes_count_idx_<n> label is used.

Examples

pmo <- read_pmo(
  system.file("extdata", "example_pmo.json.gz", package = "pmotoolsr"))
head(pmo_count_targets_per_library_sample(pmo))
#> # A tibble: 6 × 3
#>   bioinformatics_run_id                library_sample_name target_number
#>   <chr>                                <chr>                       <int>
#> 1 detected_microhaplotypes_count_idx_0 SRR30825770                    27
#> 2 detected_microhaplotypes_count_idx_0 SRR30825771                    27
#> 3 detected_microhaplotypes_count_idx_0 SRR30825772                    27
#> 4 detected_microhaplotypes_count_idx_0 SRR30825773                    27
#> 5 detected_microhaplotypes_count_idx_0 SRR30825774                    27
#> 6 detected_microhaplotypes_count_idx_0 SRR30825775                    11