R/options.default.R

In zhangh12/ARTP3: Pathway and Gene-Level Association Test

# History Jan 09 2018 Add option ambig.by.AF

options.default <- function(){
  
  opt.default <- list(out.dir = getwd(), 
                      id.str = "PID", 
                      method = 3, 
                      nperm = 1E5, 
                      snp.miss.rate = .05, 
                      maf = .05, 
                      HWE.p = 1E-5, 
                      chr.R2 = .95, 
                      gene.R2 = .95, 
                      gene.miss.rate = 1.0,                       
                      min.marg.p = 1E-7, 
                      window = 500 * 1000, 
                      group.gap = NULL, 
                      rm.gene.subset = TRUE, 
                      turn.off.filters = FALSE, 
                      impute = FALSE, 
                      delete = TRUE, 
                      print = TRUE, 
                      tidy = TRUE, 
                      save.setup = FALSE, 
                      path.setup = NULL, 
                      only.setup = FALSE, 
                      keep.geno = FALSE, 
                      seed = 1, 
                      nthread = detectCores(), 
                      excluded.snps = NULL, 
                      selected.snps = NULL, 
                      excluded.regions = NULL, 
                      excluded.subs = NULL, 
                      selected.subs = NULL, 
                      excluded.genes = NULL, 
                      meta = FALSE, 
                      only.meta = TRUE, 
                      inspect.snp.n = 5, 
                      inspect.snp.percent = 0, 
                      inspect.gene.n = 10, 
                      inspect.gene.percent = .05, 
                      trim.huge.chr = TRUE, 
                      huge.gene.size = 1000, 
                      huge.chr.size = 2000, 
                      huge.gene.R2 = .85, 
                      huge.chr.R2 = .85, 
                      min.n = FALSE, 
                      ambig.by.AF = FALSE,
                      version = packageVersion('ARTP2'))
  
  opt.default
  
}