Skip to contents

Read STRmix Kit Settings

read_STRmix_kit_settings.Rd

Read STRmix kit settings from an XML file and associated stutter directory.

Usage

read_STRmix_kit_settings(filename, stutters_dir, include_y_loci = FALSE)

Arguments

filename

Character vector specifying the path to the XML file containing the profiling kit settings.

stutters_dir

Character vector specifying the directory path where stutter settings files are located.

include_y_loci

Should Y loci be included in the list of locus names? Default is FALSE.

Value

A list containing the following components:

  • locus_names. Character vector.

  • degradation_parameter_cap. Numeric.

  • c2_prior. Numeric of length two with shape and scale.

  • LSAE_variance_prior. Numeric of length one.

  • detection_threshold. Numeric vector (named) with Detection Thresholds. Defaults to 50 for each locus.

  • size_regression. Function, see read_size_regression.

  • stutter_model. A list representing the stutter model.

  • stutter_variability. A list representing the stutter variability.