Run MixDeR workflow — run_workflow • mixder

Runs workflow

Usage

run_workflow(
  date,
  id,
  replicate_id,
  twofreqs,
  freq_both,
  freq_major,
  freq_minor,
  refData,
  refs,
  sample_path,
  output,
  run_mixdeconv,
  unconditioned,
  cond,
  method,
  sets,
  kinpath,
  dynamicAT,
  staticAT,
  minimum_snps,
  A1_threshold,
  A2_threshold,
  A1min,
  A1max,
  A2min,
  A2max,
  major,
  minor,
  minor_threshold,
  keep_bins,
  filter_missing
)

Arguments

date: date and time of run
id: Sample ID
replicate_id: Sample ID of replicate, if specified
twofreqs: TRUE if using separate AF data for major and minor contributors
freq_both: 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
refData: Reference data (if available)
refs: Path of reference genotype(s) file
sample_path: Path of sample manifest
output: Name of output directory
run_mixdeconv: TRUE if running EFM mixture deconvolution
unconditioned: TRUE if running unconditioned mixture deconvolution
cond: Sample IDs to condition on
method: Calculate Metrics or Create GEDmatch PRO Report
sets: Number of SNP sets
kinpath: Path of Kintelligence Sample Reports
dynamicAT: Dynamic AT
staticAT: Static AT
minimum_snps: Minimum number of SNPs for creating GEDmatch PRO reports
A1_threshold: Allele 1 probability threshold for creating GEDmatch PRO reports
A2_threshold: Allele 2 probability threshold for creating GEDmatch PRO reports
A1min: Minimum value for allele 1 probability thresholds for calculating metrics
A1max: Maximum value for allele 1 probability thresholds for calculating metrics
A2min: Minimum value for allele 2 probability thresholds for calculating metrics
A2max: Maximum value for allele 2 probability thresholds for calculating metrics
major: Major contributor ID
minor: Minor contributor ID
minor_threshold: If apply the allele 1 probability threshold to the minor contributor
keep_bins: To use existing SNP bins or create new bins (and files)
filter_missing: TRUE/FALSE whether to filter SNPs with either allele missing