run.threshold.scans: Runs threshold scans from a matrix of outcomes, either...

View source: R/sampling.processes.R

run.threshold.scansR Documentation

Runs threshold scans from a matrix of outcomes, either parametric bootstraps from the null model or permutations

Description

This function takes an object produced from generate.sample.outcomes.matrix(), and runs genome scans on the outcomes contained in them.

Usage

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

Arguments

sim.threshold.object

An object created by either generate.sample.outcomes.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 June 13, 2022, 4:20 p.m.