Count specimens by complexity of infection (COI)

Reads per-specimen COI values, rounds them to integers, and returns the count and proportion of specimens at each COI level.

Usage

count_samples_by_coi(coi_table, output = NULL)

Arguments

coi_table

Path to a COI table TSV, or a data frame with the same columns. See Inputs.

output

Optional output TSV path. Default for the CLI is coi_distribution.tsv.

Value

A tibble with columns coi, n, and proportion.

Details

Inputs

• coi_table: COI table (specimen_name, coi), as a file path or data frame. See vignette("input-formats", package = "PGEcore").

Outputs

• output (optional): TSV with columns coi, n, and proportion. If NULL, results are returned without writing a file.

Running

count_samples_by_coi(
  coi_table = "coi_table.tsv",
  output = "coi_distribution.tsv"
)

Rscript exec/count_samples_by_coi \
  --coi_table coi_table.tsv \
  --output coi_distribution.tsv

See also

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

Examples

coi_path <- system.file("extdata", "example_coi_table.tsv", package = "PGEcore")
count_samples_by_coi(coi_path)
#> # A tibble: 3 × 3
#>     coi     n proportion
#>   <dbl> <int>      <dbl>
#> 1     1     0        0  
#> 2     2     1        0.2
#> 3     3     4        0.8