run.simple.permutation.threshold.scans: Runs threshold scans from a matrix of permutation indexes

In gkeele/miqtl: Suite of QTL Mapping Functions

Runs threshold scans from a matrix of permutation indexes

Description

This function takes an object produced from generate.simple.permutation.index.matrix, and runs genome scans based on the permutation indexes contained in them.

Usage

run.simple.permutation.threshold.scans(
  sim.threshold.object,
  keep.full.scans = TRUE,
  scan.index = NULL,
  genomecache,
  formula,
  data,
  model = c("additive", "full"),
  use.multi.impute = TRUE,
  num.imp = 11,
  chr = "all",
  just.these.loci = NULL,
  scan.seed = 1,
  ...
)

Arguments

sim.threshold.object	An object created by generate.simple.permutation.index.matrix().
keep.full.scans	DEFAULT: TRUE. Returns full genome scans for every outcome sample in the sim.threshold.object. Can be used for visualization of the procedure, but greatly increases the size of the output object.
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.
data	A data frame with outcome and potential covariates. Should also have IDs that link to IDs in the genome cache, often the individual-level ID named "SUBJECT.NAME".
use.multi.impute	DEFAULT: TRUE. This option specifies whether to use ROP or multiple imputations.
num.imp	DEFAULT: 11. IF multiple imputations are used, this specifies the number of imputations to perform.
chr	DEFAULT: "all". The chromosomes to conduct scans over.
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.
scan.seed	DEFAULT: 1. The sampling process is random, thus a seed must be set for samples to be consistent across machines.

Examples

run.threshold.scans()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.