include.hotspots

Generate hotspots for the simulated examples in the manuscript.

Functions to infer co-mapping trait hotspots and causal models.
Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012)
Quantile-based permutation thresholds for QTL hotspots. Genetics 191 : 1355-1365.
<doi:10.1534/genetics.112.139451>.
Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2013)
Modeling causality for pairs of phenotypes in system genetics. Genetics 193 : 1003-1013.
<doi:10.1534/genetics.112.147124>.

Brian Yandell

qtlhot

Inference for QTL Hotspots

include.hotspots function

<dl><dt>cross</dt>
<dd>cross object</dd>
<dt>hchr</dt>
<dd>character string for chromosome</dd>
<dt>hpos</dt>
<dd>position on chromosome</dd>
<dt>hsize</dt>
<dd>size</dd>
<dt>Q.eff</dt>
<dd>Q effect</dd>
<dt>latent.eff</dt>
<dd>latent effect</dd>
<dt>lod.range.1</dt>
<dd>lod range 1</dd>
<dt>lod.range.2</dt>
<dd>lod range 2</dd>
<dt>lod.range.3</dt>
<dd>lod range 3</dd>
<dt>res.var</dt>
<dd>residual variance</dd>
<dt>n.pheno</dt>
<dd>number of phenotypes</dd>
<dt>init.seed</dt>
<dd>initial seed</dd></dl>

Arguments

Generate hotspots for the simulated examples in the manuscript. — include.hotspots

<dl>

<dt>cross</dt>
<dd>cross object</dd>


<dt>hchr</dt>
<dd>character string for chromosome</dd>


<dt>hpos</dt>
<dd>position on chromosome</dd>


<dt>hsize</dt>
<dd>size</dd>


<dt>Q.eff</dt>
<dd>Q effect</dd>


<dt>latent.eff</dt>
<dd>latent effect</dd>


<dt>lod.range.1</dt>
<dd>lod range 1</dd>


<dt>lod.range.2</dt>
<dd>lod range 2</dd>


<dt>lod.range.3</dt>
<dd>lod range 3</dd>


<dt>res.var</dt>
<dd>residual variance</dd>


<dt>n.pheno</dt>
<dd>number of phenotypes</dd>


<dt>init.seed</dt>
<dd>initial seed</dd>

</dl>

include.hotspots: Generate hotspots for the simulated examples in the manuscript.

Description

Usage

Arguments