radiator_dots: radiator_dots

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

radiator_dots

Description

Extract and assign the dots-dots-dots

Usage

radiator_dots(
  func.name = as.list(sys.call())[[1]],
  fd = NULL,
  args.list = NULL,
  dotslist = NULL,
  keepers = c("subsample.markers.stats", "force.stats", "id.stats", "subsample",
    "filter.reproducibility", "filter.individuals.missing",
    "filter.individuals.heterozygosity", "filter.individuals.coverage.total",
    "filter.individuals.coverage.median", "filter.individuals.coverage.iqr",
    "filter.common.markers", "filter.monomorphic", "filter.ma", "ma.stats",
    "filter.coverage", "dp", "filter.genotyping", "filter.snp.position.read",
    "filter.snp.number", "filter.short.ld", "filter.long.ld", "long.ld.missing",
    "ld.method", 
     "ld.figures", "detect.mixed.genomes",
    "ind.heterozygosity.threshold", "detect.duplicate.genomes", "filter.hwe",
    "filter.strands", "random.seed", "path.folder", "filename", "parameters",
    "blacklist.genotypes", "erase.genotypes", "gt", "gt.bin", "gt.vcf", "gt.vcf.nuc",
    "pop.levels", "pop.labels", "pop.select", "blacklist.id", "markers.info",
    "keep.allele.names", "keep.gds", "calibrate.alleles", "vcf.metadata", "vcf.stats",
    "wide", "whitelist.markers", "write.tidy", "missing.memory", "dart.sequence", 
    
    "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart", "species",
    "population", "tau", "threshold.y.markers", "threshold.y.silico.markers",
    "sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD",
    "threshold.x.markers.RD.silico", "mis.threshold.data", "mis.threshold.silicodata",
    "zoom.data", "zoom.silicodata", "sex.id.input", "het.qr.input"),
  deprecated = c("maf.thresholds", "common.markers", "max.marker", "monomorphic.out",
    "snp.ld", "filter.call.rate", "filter.markers.coverage", "filter.markers.missing",
    "number.snp.reads", "mixed.genomes.analysis", "duplicate.genomes.analysis",
    "ref.calibration"),
  verbose = TRUE
)

Arguments

func.name	Default: as.list(sys.call())[[1]].
fd	(optional) Default: rlang::fn_fmls_names().
args.list	(optional) Default:args.list = as.list(environment()).
dotslist	The dots dots dots arguments captured. Default: dotslist = rlang::dots_list(..., .homonyms = "error", .check_assign = TRUE).
keepers	(optional) The arguments that are used inside the function. Default: keepers = c( "subsample.markers.stats", "subsample", "filter.reproducibility", "filter.individuals.missing", "filter.individuals.heterozygosity", "filter.individuals.coverage.total", "filter.individuals.coverage.median", "filter.individuals.coverage.iqr", "filter.common.markers", "filter.monomorphic", "filter.ma", "ma.stats" "filter.coverage", "filter.genotyping", "filter.snp.position.read", "filter.snp.number", "filter.short.ld", "filter.long.ld", "long.ld.missing", "ld.method", "detect.mixed.genomes", "ind.heterozygosity.threshold", "detect.duplicate.genomes", "filter.hwe", "filter.strands", "random.seed", "path.folder", "filename", "blacklist.genotypes", "erase.genotypes", "gt", "gt.bin", "gt.vcf", "gt.vcf.nuc", "pop.levels", "pop.labels", "pop.select", "blacklist.id", "markers.info", "keep.allele.names", "keep.gds", "calibrate.alleles", "vcf.metadata", "vcf.stats", "id.stats", "dp", "whitelist.markers", "write.tidy", "dart.sequence", "missing.memory", "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart", "species", "population", "tau", "threshold.y.markers", "threshold.y.silico.markers", "sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD", "threshold.x.markers.RD.silico", "mis.threshold.data", "mis.threshold.silicodata", "zoom.data", "zoom.silicodata", "sex.id.input", "het.qr.input").
deprecated	(optional) radiator's deprecated arguments. Default: deprecated = c("maf.thresholds", "common.markers", "max.marker","monomorphic.out", "snp.ld", "filter.call.rate", "filter.markers.coverage", "filter.mac","filter.markers.missing", "number.snp.reads", "mixed.genomes.analysis", "duplicate.genomes.analysis", "maf.data", "ref.calibration").
verbose	(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.