run MixDeR using the CLI; calculate validation metrics

Usage

run_mixder_metrics(
  sample_manifest = NULL,
  sample = NULL,
  replicate = NULL,
  sample_reports = getwd(),
  output = "output",
  twofreqs = FALSE,
  freq_both = "global_1000g",
  freq_major = NULL,
  freq_minor = NULL,
  refpath = NULL,
  refs = NULL,
  mixdeconv = TRUE,
  uncond = TRUE,
  cond = FALSE,
  sets = 10,
  dynamicAT = 0.015,
  staticAT = 10,
  minimum_snps = 6000,
  A1min = 0.95,
  A1max = 0.99,
  A2min = 0.5,
  A2max = 0.65,
  major = NULL,
  minor = NULL,
  filter_missing = FALSE,
  minor_contrib_threshold = FALSE,
  keep_bins = TRUE
)

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")
twofreqs: TRUE if using different allele frequency data for each contributor (default=FALSE)
freq_both: frequency data for both contributors; requires twofreqs=FALSE (default=1000G global)
freq_major: frequency data for major contributor; requires twofreqs=TRUE (default=NULL)
freq_minor: frequency data for minor contributor; requires twofreqs=TRUE (default=NULL)
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)
A1min: when calculating metrics, the start of the range of the allele 1 probability threshold (default=0.95)
A1max: when calculating metrics, the end of the range of the allele 1 probability threshold (default=0.99)
A2min: when calculating metrics, the start of the range of the allele 2 probability threshold (default=0.50)
A2max: when calculating metrics, the end of the range of the allele 2 probability threshold (default=0.65)
major: for comparing references to generated single source profiles, the assumed major contributor sample ID (default=NULL)
minor: for comparing references to generated single source profiles, the assumed minor contributor sample ID (default=NULL)
filter_missing: Whether to remove SNPs with a missing value for the allele 2 (default=FALSE)
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)