Create configuration file containing all settings for a specific run

Usage

create_config(
  date,
  twofreqs,
  freq_all,
  freq_major,
  freq_minor,
  refs,
  sample_path,
  out_path,
  run_mixdeconv,
  unconditioned,
  cond,
  method,
  sets,
  kinpath,
  dynamicAT,
  staticAT,
  minimum_snps,
  A1_threshold,
  A2_threshold,
  A1min,
  A1max,
  A2min,
  A2max,
  major,
  minor,
  filter_missing
)

Arguments

date: date and time of run
twofreqs: TRUE if using separate AF data for major and minor contributors
freq_all: Path (or name) of allele frequency data if using same data for both
freq_major: Path (or name) of allele frequency data for major contributor
freq_minor: Path (or name) of allele frequency data for minor contributor
refs: path to reference folder
sample_path: path to sample manifest
out_path: name of output folder
run_mixdeconv: if running mixture deconvolution
unconditioned: if running an unconditioned deconvolution
cond: if running a conditioned deconvolution, which references to condition on
method: downstream method (calculate metrics/create GEDmatch PRO report)
sets: number of SNP sets
kinpath: path to mixture (evidence) files
dynamicAT: dynamic AT
staticAT: static AT
minimum_snps: minimum number of SNPs
A1_threshold: Allele 1 probability threshold for GEDmatch PRO report creation
A2_threshold: Allele 2 probability threshold for GEDmatch PRO report creation
A1min: minimum allele 1 probability threshold in range for calculating metrics
A1max: maximum allele 1 probability threshold in range for calculating metrics
A2min: minimum allele 2 probability threshold in range for calculating metrics
A2max: maximum allele 2 probability threshold in range for calculating metrics
major: assumed major contributor of mixture
minor: assumed minor contributor of mixture
filter_missing: TRUE/FALSE whether to filter SNPs if second allele is missing (99)