run.perm.scans: Runs permutation scans from a permutation index matrix,...
In gkeele/sparcc: Simulated Power Analysis in the Realized Collaborative Cross

This function takes the outputs from generate.perm.matrix(), sim.CC.data(), and run.sim.scans() to perform permutation scans and determine a significance threshold.

run.perm.scans(perm.matrix, sim.CC.scans, sim.CC.object,
  phenotype.index = NULL, all.sim.qr = NULL, scan.index = NULL,
  chr = "all", just.these.loci = NULL, use.progress.bar = FALSE,
  print.scans.progress = FALSE, ...)

`perm.matrix`	Permutation index matrix that is output from generate.perm.matrix().
`sim.CC.scans`	Genome scans from simulated CC data output from run.sim.scans().
`sim.CC.object`	Simulated CC data output from sim.CC.data().
`phenotype.index`	The phenotype index of simulated phenotype that correspond to those found in sim.CC.scans and sim.CC.objects.
`all.sim.qr`	DEFAULT: NULL. Allows qr decompositions to only be saved once. If NULL, it expects that they are stored in sim.CC.scans$all.sim.qr, which can be specified in run.sim.scans().
`scan.index`	DEFAULT: NULL. If NULL, it performs scans for all permuted data sets based on permutation index. If given a vector of integers, representing the permutation index, it will only run scans for those permutations.
`chr`	DEFAULT: "all". Specifies which chromosomes to scan.
`just.these.loci`	DEFAULT: NULL. If NULL, all loci in genome cache are scanned.
`use.progress.bar`	DEFAULT: FALSE. Specifies whether to use a progress bar for qr decompositions and genome scans.
`print.scans.progress`	DEFAULT: FALSE. Specifies whether to output a message that indicates the number of permutation scans completed.