Process real data

Generate the COI curve for real data.

Usage

process_real(
  wsmaf,
  plmaf,
  coverage,
  seq_error = 0.01,
  bin_size = 20,
  coi_method = "variant"
)

Arguments

wsmaf

The within-sample minor allele frequency.

plmaf

The population-level minor allele frequency.

coverage

The read coverage at each locus.

seq_error

The level of sequencing error that is assumed. If no value is inputted, then we infer the level of sequence error.

bin_size

This argument is no longer supported; to estimate the COI, all data points are used. Data points are not grouped in bins of changing plaf.

coi_method

The method we will use to generate the theoretical relationship. The method is either "variant" or "frequency". The default value is "variant".

Value

A list of the following:

• data: A tibble with

• plmaf_cut: Breaks of the form [a, b).

• m_variant: The average WSMAF or proportion of variant sites in each segment defined by plmaf_cut.

• bucket_size: The number of loci in each bucket.

• midpoints: The midpoint of each bucket.

• seq_error: The sequence error inferred.

• bin_size: The minimum size of each bin.

• cuts: The breaks utilized in splitting the data. of each COI.

Details

The function computes whether a SNP is a variant site or not, based on the WSMAF at that SNP. This process additionally accounts for potential sequencing error.

See also

process_sim() to process simulated data.