Summarise alleles per target in positive controls

Summarise alleles per target in positive controls

Usage

summarise_positive_controls(
  allele_data_qc,
  manifest,
  allele_col = "pseudocigar_masked",
  read_filter = 0,
  af_filter = 0.01
)

Arguments

allele_data_qc

Allele data with targets excluded from QC removed and AlleleFreq added (see add_allele_frequency()).

manifest

Manifest from read_manifest().

allele_col

Column used as the allele ID, "asv" or "pseudocigar_masked". With "pseudocigar_masked" alleles are collapsed to unique masked pseudocigars.

read_filter

Minimum reads for an allele to be counted.

af_filter

Minimum within-sample allele frequency for an allele to be counted.

Value

A list with locus_summary (alleles per target per control), category_counts (targets per allele category per control) and polyclonal_information (alleles at multiallelic targets).