Read Mad4hatter results — read_mad4hatter

Reads the outputs needed for QC from a Mad4hatter results directory. sample_coverage.txt, amplicon_coverage.txt, allele_data.txt and panel_information/amplicon_info.tsv are required. The collapsed allele table and the resistance marker tables are read if present and are NULL otherwise.

Usage

read_mad4hatter_results(
  results_dir,
  standardise_sample_name = TRUE,
  manifest_sample_names = character()
)

Arguments

results_dir: Path to the Mad4hatter results directory.
standardise_sample_name: If TRUE, Illumina suffixes are removed from sample names with standardise_illumina_sample_name() so they match the manifest. A warning is given if this makes different sample names identical.
manifest_sample_names: Sample names from the manifest. Names that already match exactly are not trimmed.

Value

A named list of data frames: sample_coverage, amplicon_coverage, allele_data, panel_information, collapsed_allele_data, resmarker_table and resmarker_microhaplotype_table.