instability.lm.scan: Runs quick fixed effect only scans off of simple bootstrap...
In gkeele/kqtl: Suite of QTL Mapping Functions

Description Usage Arguments Examples

This function runs scans of simple bootstraps or permutations from a data set with the purpose of assessing the null distribution of the p-values.

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instability.lm.scan(simple.sample.object, genomecache, model = c("additive",
  "full"), seed = 1, use.ROP = TRUE, num.imp = 11, chr = "all",
  just.these.loci = NULL, print.locus.fit = TRUE, ...)

`simple.sample.object`	An object returned from generate.simple.sample.outcomes.matrix(). This contains the samples and supporting information for the fast scans.
`genomecache`	The path to the genome cache directory. The genome cache is a particularly structured directory that stores the haplotype probabilities/dosages at each locus. It has an additive model subdirectory and a full model subdirectory. Each contains subdirectories for each chromosome, which then store .RData files for the probabilities/dosages of each locus.
`model`	DEFAULT: additive. Specifies how to model the founder haplotype probabilities. The additive options specifies use of haplotype dosages, and is most commonly used. The full option regresses the phenotype on the actual diplotype probabilities.
`seed`	DEFAULT: 1. The sampling process is random, thus a seed must be set for samples to be consistent across machines.
`use.ROP`	DEFAULT: TRUE. TRUE specifies ROP. FALSE specifies multiple imputations.
`num.imp`	DEFAULT: 11. The number of imputations that are used.
`chr`	DEFAULT: "all". Specifies which chromosomes to scan.
`just.these.loci`	DEFAULT: NULL. Specifies a reduced set of loci to fit. If loci is just one locus, the alternative model fit will also be output as fit1.
`print.locus.fit`	DEFAULT: TRUE If TRUE, prints out how many loci have been fit currently.