generate.qr.permutation.index.matrix: Outputs a matrix of permuted indeces for permutation scans,...

In gkeele/miqtl: Suite of QTL Mapping Functions

Outputs a matrix of permuted indeces for permutation scans, allowing for the same permutations of individuals across different outcomes.

Description

This function produces a matrix with columns that represent the permutations of the row index of the phenotype data. This allows the same permutations of individuals to be used across different phenotypes. This approach is only statistically valid when individuals are exchangeable.

Usage

generate.qr.permutation.index.matrix(
  qr.scan.object = NULL,
  n = NULL,
  num.samples,
  seed = 1
)

Arguments

qr.scan.object	DEFAULT: NULL. Output object from scan.qr(). If NULL, function expects the number of individuals being permutated.
n	DEFAULT: NULL. Alternative to qr.scan.object. If NULL, function expects a qr.scan object.
num.samples	The number of permutations of the index to create - ultimately the number of columns in the output matrix.
seed	DEFAULT: 1. Samplings of the index is a random process, thus a seed is necessary to produce the same results over multiple runs and different machines.

Examples

generate.qr.permutation.index.matrix()

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