Estimate complexity of infection (COI) using coiaf

Processes SNP read-count data and optionally population-level minor allele frequencies (PLMAF), then estimates COI with both the frequency and variant methods from the coiaf package (Suggests; not installed with PGEcore).

Usage

run_coiaf(snp_calls, plmaf = NULL, seq_error = 0.01, max_coi = 25)

Arguments

snp_calls: SNP-calls data frame. See Inputs.
plmaf: Optional PLMAF data frame. See Inputs.
seq_error: Sequencing error rate (default: 0.01).
max_coi: Maximum COI to consider (default: 25).

Value

A data frame with columns specimen_name, coi_freq, and coi_variant.

Details

Inputs

snp_calls: SNP-calls data frame (specimen_name, snp_name, reads, seq_base). See vignette("input-formats", package = "PGEcore").
plmaf: Optional PLMAF data frame (snp_name, seq_base, plmaf). If NULL, PLMAF is calculated from snp_calls.

Outputs

Returns a data frame with specimen_name, coi_freq, and coi_variant (not written to disk). For file I/O, use coiaf_wrapper().

Running

run_coiaf(snp_calls = snp_df, plmaf = plmaf_df)

File and CLI users should call coiaf_wrapper() / Rscript exec/coiaf_wrapper ....

Requires coiaf (Suggests).