scanonevar.meanperm

Executes permutations of the genotypes in the mean-effect part of scanonevar

Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.

Karl Broman

Tools for Analyzing QTL Experiments

scanonevar.meanperm function

<dl> <dt>cross</dt>
<dd>An object of class <code>cross</code>. See
 <code>read.cross</code> for details.</dd> <dt>pheno.col</dt>
<dd>Column number in the phenotype matrix which should be
 used as the phenotype. This must be a single value (integer index or
 phenotype name) or a numeric vector of
 phenotype values, in which case it must have the length equal to the number
 of individuals in the cross, and there must be either non-integers or
 values &lt; 1 or &gt; no. phenotypes; this last case may be useful for studying
 transformations.</dd> <dt>mean_covar</dt>
<dd>Numeric matrix with covariates affecting the mean.</dd> <dt>var_covar</dt>
<dd>Numeric matrix with covariates affecting the variances.</dd> <dt>maxit</dt>
<dd>Maximum number of iterations in the algorithm to fit the
 model at a given position.</dd> <dt>tol</dt>
<dd>Tolerance for convergence.</dd> <dt>n.mean.perm</dt>
<dd>Numeric vector of length one indicates the number of permutations to execute.</dd> <dt>seed</dt>
<dd>Numeric vector of length one indicates the random seed to start the permutations.</dd> <dt>quiet</dt>
<dd>If <code>FALSE</code>, print some information about the course
 of the calculations.</dd></dl>

Arguments

Permutation test for mean effect in scanonevar — scanonevar.meanperm

<dl>

 <dt>cross</dt>
<dd>An object of class <code>cross</code>. See
 <code>read.cross</code> for details.</dd>

 <dt>pheno.col</dt>
<dd>Column number in the phenotype matrix which should be
 used as the phenotype. This must be a single value (integer index or
 phenotype name) or a numeric vector of
 phenotype values, in which case it must have the length equal to the number
 of individuals in the cross, and there must be either non-integers or
 values &lt; 1 or &gt; no. phenotypes; this last case may be useful for studying
 transformations.</dd>

 <dt>mean_covar</dt>
<dd>Numeric matrix with covariates affecting the mean.</dd>

 <dt>var_covar</dt>
<dd>Numeric matrix with covariates affecting the variances.</dd>

 <dt>maxit</dt>
<dd>Maximum number of iterations in the algorithm to fit the
 model at a given position.</dd>

 <dt>tol</dt>
<dd>Tolerance for convergence.</dd>

 <dt>n.mean.perm</dt>
<dd>Numeric vector of length one indicates the number of permutations to execute.</dd>

 <dt>seed</dt>
<dd>Numeric vector of length one indicates the random seed to start the permutations.</dd>

 <dt>quiet</dt>
<dd>If <code>FALSE</code>, print some information about the course
 of the calculations.</dd>

</dl>

scanonevar.meanperm: Permutation test for mean effect in scanonevar

Description

Usage

Value

Arguments