Estimate allele frequency naively from AA or microhaplotype calls

Exactly one of aa_calls or allele_table must be provided. Frequency is estimated either from within-sample read-count proportions (read_count_prop) or from presence/absence (presence_absence).

Usage

estimate_allele_frequency_naive(
  aa_calls = NULL,
  allele_table = NULL,
  method = "presence_absence",
  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.
method: Estimation method: "presence_absence" (default) or "read_count_prop".
output: Optional output TSV path. Default for the CLI is allele_frequency.tsv.

Value

A tibble of estimated allele frequencies. For amino acid input the variant column is a STAVE-style gene_id:aa_position:aa string. For microhaplotype input columns include target_name, seq, and freq (plus count columns for presence_absence).

Details

Inputs

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

Outputs

output (optional): Allele-frequency TSV. For AA input, variant is a STAVE-style gene_id:aa_position:aa string plus freq (and count columns for presence_absence). For microhaplotype input: target_name, seq, freq (plus counts for presence_absence). If NULL, results are returned without writing a file.

Running

estimate_allele_frequency_naive(
  aa_calls = "aa_calls.tsv",
  output = "allele_frequency.tsv"
)

Rscript exec/estimate_allele_frequency_naive \
  --aa_calls aa_calls.tsv \
  --output allele_frequency.tsv

Examples

aa_path <- system.file(
  "extdata", "example_aa_calls.tsv",
  package = "PGEcore"
)
estimate_allele_frequency_naive(aa_calls = aa_path)
#> # A tibble: 10 × 4
#>    variant               allele_total allele_count  freq
#>    <chr>                        <int>        <int> <dbl>
#>  1 PF3D7_0417200.1:108:N            5            2 0.4  
#>  2 PF3D7_0417200.1:108:S            5            3 0.6  
#>  3 PF3D7_0417200.1:51:I             5            2 0.4  
#>  4 PF3D7_0417200.1:51:N             5            3 0.6  
#>  5 PF3D7_0417200.1:59:C             7            3 0.429
#>  6 PF3D7_0417200.1:59:R             7            4 0.571
#>  7 PF3D7_0810800.1:437:A            6            3 0.5  
#>  8 PF3D7_0810800.1:437:G            6            3 0.5  
#>  9 PF3D7_0810800.1:540:E            5            3 0.6  
#> 10 PF3D7_0810800.1:540:K            5            2 0.4