Summarize alleles per locus from an allele table

For each target_name, computes total allele count, unique allele count, and the number of alleles that appear only once (singlets).

Usage

allele_per_locus_summary(allele_table, output = "allele_summary_by_target.tsv")

Arguments

allele_table: Path to an allele table TSV. See Inputs.
output: Optional output TSV path. Defaults to "allele_summary_by_target.tsv".

Value

A tibble with columns target_name, total_allele_count, unique_allele_count, and allele_singlets.

Details

Inputs

allele_table: Allele table (specimen_name, target_name, seq). See vignette("input-formats", package = "PGEcore").

Outputs

output (optional): TSV with columns target_name, total_allele_count, unique_allele_count, and allele_singlets. Defaults to "allele_summary_by_target.tsv". If NULL, results are returned without writing a file.

Running

allele_per_locus_summary(
  allele_table = "allele_table.tsv",
  output = "allele_summary_by_target.tsv"
)

Rscript exec/allele_per_locus_summary \
  --allele_table allele_table.tsv \
  --output allele_summary_by_target.tsv

Examples

allele_path <- system.file(
  "extdata", "example_allele_table.tsv",
  package = "PGEcore"
)
allele_per_locus_summary(allele_path, output = NULL)
#> [1] "Reading input data"
#> [1] "Validating input format"
#> [1] "Confronting input data with validation rules"
#> [1] "Returning Locus data"
#> # A tibble: 5 × 4
#>   target_name             total_allele_count unique_allele_count allele_singlets
#>   <chr>                                <int>               <int>           <int>
#> 1 Pf3D7_01_v3-145388-145…                 11                   3               0
#> 2 Pf3D7_01_v3-162867-163…                 12                   3               0
#> 3 Pf3D7_01_v3-181512-181…                 11                   3               0
#> 4 Pf3D7_01_v3-194742-194…                 10                   3               0
#> 5 Pf3D7_01_v3-455794-456…                  6                   2               1