DSPRperm: DSPR permutation test

In egking/DSPRqtl: Analysis of DSPR phenotypes in R

Description

DSPRperm performs a permutation test for a DSPR dataset.

Usage

DSPRperm(model, design, phenotype.dat, id.col, batch = 1000, niter = 1000,
  alpha = 0.05, sex)

Arguments

model	an object of class formula: a symbolic description of the null model to be fitted at each position (e.g., phenotype ~ 1). The genotype effects to be fitted will be added based on design.
design	a character string. One of either 'inbredA', 'inbredB', or 'ABcross' corresponding to the pA and pB set of inbred RILs or the pA-pB cross design. For round robin designs or other cross designs, use the more flexible DSPRgenos and standard model fitting functions in R.
phenotype.dat	data.frame containing phenotype data. For inbred designs, there must be a column of numeric RIL ids (must be named patRIL). For the ABcross design, there must be both a patRIL and matRIL column specifying the pA and pB RIL ids.
id.col	a character string identifying the name of the column containing unique ids for the samples. e.g. for an inbred design, the patRIL column can be used as the id.
batch	A numeric vector of length one specifying the number of positions to be examined at a time. A larger number will use more memory but can be faster. Default is 1000.
niter	A numeric vector of length one specifying the number of permutations to run. Default is 1000.
alpha	The alpha level for the genome-wide signficance threshold. Default is 0.05. Raw maximum LOD scores are also returned and quantile can be used to test other alphas.
sex	a character string (either 'm' or 'f') specifying the sex of the measured individuals. This argument must be supplied for a cross design for correct specification of the genotypes on the X chromosome.

Details

The permutation test can take a very long time to run (over 24 hrs).

Value

A list of class pt containing:

maxLODs	A vector containing the maximum LOD score obtained for each permutation of the data.
alpha	the specified alpha level
threshold	the signficance threshold at the specified alpha level

Author(s)

Elizabeth King ([e-mail])

egking/DSPRqtl documentation built on May 16, 2019, 12:14 a.m.