Estimate multilocus prevalence and frequency with variantstring

Converts amino acid calls to variant strings, extracts unambiguous component genotypes, and estimates prevalence and frequency of each component against the full dataset.

Usage

multilocus_prevfreq_naive_variantstring(aa_calls, loci_groups, output = NULL)

Arguments

aa_calls

Path to an AA calls TSV. See Inputs.

loci_groups

Path to a loci groups TSV. See Inputs.

output

Optional path for the prev/freq TSV.

Value

A tibble with columns group_id, variant, prev, freq, and sample_total.

Details

Inputs

• aa_calls: AA calls (specimen_name, gene_id, aa_position, reads, aa). See vignette("input-formats", package = "PGEcore").

• loci_groups: Loci groups (group_id, gene_id, aa_position). See the same vignette.

Outputs

• output (optional): Prev/freq TSV with columns group_id, variant, prev, freq, and sample_total. If NULL, results are returned without writing.

Running

multilocus_prevfreq_naive_variantstring(
  aa_calls = "aa_calls.tsv",
  loci_groups = "loci_groups.tsv",
  output = "multilocus_prevfreq.tsv"
)

Rscript exec/multilocus_prevfreq_naive_variantstring \
  --aa_calls aa_calls.tsv \
  --loci_groups loci_groups.tsv \
  --output multilocus_prevfreq.tsv

Requires the optional variantstring package (Suggests). It is not installed automatically with PGEcore.

See also

vignette("input-formats", package = "PGEcore")

Examples

aa_path <- system.file(
  "extdata", "example_aa_calls.tsv",
  package = "PGEcore"
)
groups_path <- system.file(
  "extdata", "example_loci_groups.tsv",
  package = "PGEcore"
)
multilocus_prevfreq_naive_variantstring(aa_path, groups_path)
#> # A tibble: 12 × 5
#>    group_id      variant                                prev   freq sample_total
#>    <chr>         <chr>                                 <dbl>  <dbl>        <int>
#>  1 pfdhfr_pfdhps PF3D7_0417200.1:51_59_108:N_R_N;PF3D… 0.333 0.333             3
#>  2 pfdhfr_pfdhps PF3D7_0417200.1:51_59_108:N_C_S;PF3D… 0.333 0.267             3
#>  3 pfdhfr_pfdhps PF3D7_0417200.1:51_59_108:N_R_S;PF3D… 0.333 0.0667            3
#>  4 pfdhfr        PF3D7_0417200.1:51_59_108:N_R_N       0.333 0.333             3
#>  5 pfdhfr        PF3D7_0417200.1:51_59_108:N_C_S       0.333 0.267             3
#>  6 pfdhfr        PF3D7_0417200.1:51_59_108:N_R_S       0.333 0.0667            3
#>  7 pfdhfr        PF3D7_0417200.1:51_59_108:I_C_S       0.333 0.133             3
#>  8 pfdhfr        PF3D7_0417200.1:51_59_108:I_R_S       0.333 0.2               3
#>  9 pfdhps        PF3D7_0810800.1:437_540:A_E           0.333 0.333             3
#> 10 pfdhps        PF3D7_0810800.1:437_540:G_E           0.333 0.333             3
#> 11 pfdhps        PF3D7_0810800.1:437_540:A_K           0.333 0.0667            3
#> 12 pfdhps        PF3D7_0810800.1:437_540:G_K           0.333 0.267             3