mincRandomize: Run a permutation test on a 'mincLm' result

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Run a permutation test on a mincLm result

Description

Run a permutation test on a mincLm result, computing the most extreme statistic under exchanged response variables. The randomization distribution of these extremal statistics is returbed.

Usage

mincRandomize(
  x,
  R = 500,
  alternative = c("two.sided", "greater"),
  replace = FALSE,
  parallel = NULL,
  columns = grep("tvalue-", colnames(x)),
  resources = list(),
  conf_file = getOption("RMINC_BATCH_CONF")
)

## S3 method for class 'mincLm'
mincRandomize(
  x,
  R = 500,
  alternative = c("two.sided", "greater"),
  replace = FALSE,
  parallel = NULL,
  columns = grep("tvalue-", colnames(x)),
  resources = list(),
  conf_file = getOption("RMINC_BATCH_CONF")
)

Arguments

x	A mincLm object.
R	number of randomizations to perform
alternative	Whether to consider a one-sided or two-sided alternative hypothesis. Default "two-sided", use "greater" for a one sided test.
replace	Sample with or without replacement for the randomization, defaults to FALSE (no replacement)
parallel	A two component vector indicating how to parallelize the computation. If the first element is "local" the computation will be run via the parallel package, otherwise it will be computed using batchtools, see pMincApply for details. The element should be numeric indicating the number of jobs to split the computation into.
columns	Which columns to compute extrema for, defaults to columns with 'tvalue' in the name.
resources	A list of resources to use for the jobs, for example list(nodes = 1, memory = "8G", walltime = "01:00:00") . See system.file("parallel/pbs_script.tmpl", package = "RMINC") and system.file("parallel/sge_script.tmpl", package = "RMINC") for more examples
conf_file	A batchtools configuration file defaulting to getOption("RMINC_BATCH_CONF")

Value

A list with the original object, the randomization distribution of extremal statistics and configuration args used for computing the distributions.

Methods (by class)

• mincLm: mincLm

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.