run MixDeR using the CLI; ancestry prediction

Usage

run_mixder_ancestry(
  sample_manifest = NULL,
  sample = NULL,
  replicate = NULL,
  sample_reports = getwd(),
  output = "output",
  refpath = NULL,
  refs = NULL,
  mixdeconv = TRUE,
  uncond = TRUE,
  cond = FALSE,
  sets = 10,
  dynamicAT = 0.015,
  staticAT = 10,
  minimum_snps = 6000,
  A1_threshold = 0.99,
  A2_threshold = 0.6,
  minor_contrib_threshold = FALSE,
  keep_bins = TRUE,
  snps,
  pcagroups
)

Arguments

sample_manifest: path to sample manifest file (default=NULL)
sample: If running individual sample, specify the sample ID; requires sample_manifest=NULL (default=NULL)
replicate: If running individual sample along with a replicate, specify the replicate ID; requires sample_manifest=NULL (default=NULL)
sample_reports: Path to directory of Sample Reports or CSV file of mixture genotypes (default=current directory)
output: name of output directory, will be outputted into the sample reports directory (default="output")
refpath: Path to directory containing reference genotypes (default=NULL)
refs: list of sample IDs to use as reference for conditioning, can specify more than one (default=NULL, example: list("Ref1", "Ref2"))
mixdeconv: whether to run mixture deconvolution (default=TRUE)
uncond: run (or use) an unconditioned mixture deconvolution (default=TRUE)
cond: run (or use) a conditioned mixture deconvolution (default=FALSE)
sets: number of bins to divide SNPs into (default=10)
dynamicAT: dynamic analytical threshold applied to data (default=0.015)
staticAT: static analytical threshold applied to data (default=10)
minimum_snps: minimum number of SNPs used to generate profile (default=6000)
A1_threshold: Allele 1 probability threshold (default=0.99)
A2_threshold: Allele 2 probability threshold (default=0.60)
minor_contrib_threshold: Whether to apply the allele 1 probability threshold to the minor contributor, regardless of the minimum number of SNPs (default=FALSE)
keep_bins: Use existing binned SNP data, if exists (default=TRUE)
snps: SNPs to use for ancestry prediction (either ancestry only or all SNPs)
pcagroups: How to color PCA plots (superpopulations and/or subpopulations)