Estimate allele prevalence naively from AA or microhaplotype calls

Exactly one of aa_calls or allele_table must be provided. Prevalence is the fraction of specimens carrying each allele at a locus.

Usage

estimate_allele_prevalence_naive(
  aa_calls = NULL,
  allele_table = NULL,
  output = NULL
)

Arguments

aa_calls: Optional path to an AA calls TSV. See Inputs.
allele_table: Optional path to an allele table TSV. See Inputs.
output: Optional output TSV path. Default for the CLI is prevalence.tsv.

Value

A tibble of allele prevalences. For amino acid input: variant, prev, sample_count, sample_total. For microhaplotype input: target_name, seq, prev, sample_count, sample_total.

Details

Inputs

aa_calls (optional): AA calls (specimen_name, gene_id, aa_position, aa). See vignette("input-formats", package = "PGEcore").
allele_table (optional): Allele table (specimen_name, target_name, seq). See the same vignette.

Outputs

output (optional): Prevalence TSV. For AA input: variant, prev, sample_count, sample_total. For microhaplotype input: target_name, seq, prev, sample_count, sample_total. If NULL, results are returned without writing a file.

Running

estimate_allele_prevalence_naive(
  aa_calls = "aa_calls.tsv",
  output = "prevalence.tsv"
)

Rscript exec/estimate_allele_prevalence_naive \
  --aa_calls aa_calls.tsv \
  --output prevalence.tsv

Examples

aa_path <- system.file(
  "extdata", "example_aa_calls.tsv",
  package = "PGEcore"
)
estimate_allele_prevalence_naive(aa_calls = aa_path)
#> # A tibble: 10 × 4
#>    variant                prev sample_count sample_total
#>    <chr>                 <dbl>        <int>        <int>
#>  1 PF3D7_0417200.1:108:N  0.5             2            4
#>  2 PF3D7_0417200.1:108:S  0.75            3            4
#>  3 PF3D7_0417200.1:51:I   0.5             2            4
#>  4 PF3D7_0417200.1:51:N   0.75            3            4
#>  5 PF3D7_0417200.1:59:C   0.75            3            4
#>  6 PF3D7_0417200.1:59:R   1               4            4
#>  7 PF3D7_0810800.1:437:A  0.75            3            4
#>  8 PF3D7_0810800.1:437:G  0.75            3            4
#>  9 PF3D7_0810800.1:540:E  0.75            3            4
#> 10 PF3D7_0810800.1:540:K  0.5             2            4