pValue

P-value graph to determine threshold for marker clustering

misc

Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).

Julian Taylor

ASMap

Linkage Map Construction using the MSTmap Algorithm

pValue function

<dl><dt>dist</dt>
<dd>Numeric range of genetic distances in cM.</dd><dt>pop.size</dt>
<dd>Numeric range of population sizes.</dd><dt>map.function</dt>
<dd>Character string of either <code>"koasmbi"</code>, <code>"haldane"</code>,
<code>"morgan"</code> or <code>"cf"</code> defining the mapping function to be used.</dd><dt>LOD</dt>
<dd>If <code>LOD = TRUE</code> the LOD score of linkage is calculated
or if <code>LOD = FALSE</code> then the minus log10 p-value used to threshold the
hoeffding inequality is calculated (defaults to <code>FALSE</code>).</dd></dl>

Arguments

Author

P-value graph — pValue

<dl>

<dt>dist</dt>
<dd>Numeric range of genetic distances in cM.</dd>

<dt>pop.size</dt>
<dd>Numeric range of population sizes.</dd>

<dt>map.function</dt>
<dd>Character string of either <code>"koasmbi"</code>, <code>"haldane"</code>,
<code>"morgan"</code> or <code>"cf"</code> defining the mapping function to be used.</dd>

<dt>LOD</dt>
<dd>If <code>LOD = TRUE</code> the LOD score of linkage is calculated
or if <code>LOD = FALSE</code> then the minus log10 p-value used to threshold the
hoeffding inequality is calculated (defaults to <code>FALSE</code>).</dd>

</dl>

pValue: P-value graph

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples