Running mixture deconvolution in EuroForMix

Usage

run_efm(
  date,
  popFreq,
  refData,
  id,
  replicate_id,
  inpath,
  out_path,
  attable,
  nsets,
  cond = NULL,
  uncond = TRUE,
  keep_bins = TRUE
)

Arguments

date: Date and time of MixDeR run
popFreq: Allele frequency file
refData: Reference genotypes file
id: Sample ID
replicate_id: Replicate ID
inpath: Path to SNP sets
out_path: Output path
attable: AT table
nsets: Number of SNP sets
cond: Sample IDs to condition on
uncond: TRUE/FALSE if performing unconditioned analysis
keep_bins: To use existing SNP bins or create new bins (and files)