Filter amino acid calls to biallelic loci

Keeps loci (gene_id, aa_position, ref_aa) with at most two distinct aa alleles. Optionally writes non-biallelic loci to a second file.

Usage

filter_biallelic_calls(
  aa_calls,
  output = NULL,
  nonbiallelic_output = NULL,
  overwrite = FALSE
)

Arguments

aa_calls: Path to an AA calls TSV, or a data frame with the same columns. See Inputs.
output: Optional path for the biallelic output TSV.
nonbiallelic_output: Optional path for loci with more than two alleles.
overwrite: If FALSE (default), refuse to overwrite existing outputs.

Value

A list with tibbles biallelic and nonbiallelic. Each includes an allele_calls column with the distinct allele count per locus.

Details

Inputs

aa_calls: AA calls (gene_id, aa_position, ref_aa, aa), as a file path or data frame. See vignette("input-formats", package = "PGEcore").

Outputs

output (optional): Biallelic AA calls TSV (includes allele_calls).
nonbiallelic_output (optional): Non-biallelic loci TSV (includes allele_calls).

Running

filter_biallelic_calls(
  aa_calls = "aa_calls.tsv",
  output = "biallelic_aa_calls.tsv"
)

Rscript exec/filter_biallelic_calls \
  --aa_calls aa_calls.tsv \
  --output biallelic_aa_calls.tsv

Examples

path <- system.file("extdata", "example_aa_calls.tsv", package = "PGEcore")
filter_biallelic_calls(path)
#> $biallelic
#> # A tibble: 28 × 10
#>    specimen_name target_name    reads gene   aa_locus gene_id aa_position ref_aa
#>    <chr>         <chr>          <dbl> <chr>  <chr>    <chr>         <dbl> <chr> 
#>  1 specimen1     pfdhfr_1_150       5 dhfr-… PF3D7_0… PF3D7_…          51 N     
#>  2 specimen1     pfdhfr_1_150       5 dhfr-… PF3D7_0… PF3D7_…          59 C     
#>  3 specimen1     pfdhfr_1_150       5 dhfr-… PF3D7_0… PF3D7_…         108 S     
#>  4 specimen1     pfdhps_400_550     5 dhps   PF3D7_0… PF3D7_…         437 A     
#>  5 specimen1     pfdhps_400_550     5 dhps   PF3D7_0… PF3D7_…         540 K     
#>  6 specimen2     pfdhfr_1_150       5 dhfr-… PF3D7_0… PF3D7_…          51 N     
#>  7 specimen2     pfdhfr_1_150       4 dhfr-… PF3D7_0… PF3D7_…          59 C     
#>  8 specimen2     pfdhfr_1_150       1 dhfr-… PF3D7_0… PF3D7_…          59 C     
#>  9 specimen2     pfdhfr_1_150       5 dhfr-… PF3D7_0… PF3D7_…         108 S     
#> 10 specimen2     pfdhps_400_550     5 dhps   PF3D7_0… PF3D7_…         437 A     
#> # ℹ 18 more rows
#> # ℹ 2 more variables: aa <chr>, allele_calls <int>
#> 
#> $nonbiallelic
#> # A tibble: 0 × 10
#> # ℹ 10 variables: specimen_name <chr>, target_name <chr>, reads <dbl>,
#> #   gene <chr>, aa_locus <chr>, gene_id <chr>, aa_position <dbl>, ref_aa <chr>,
#> #   aa <chr>, allele_calls <int>
#>