snpinfo_to_map

Routines in 'qtl2' to study allele patterns in quantitative trait loci (QTL)
mapping over a chromosome.
Useful in crosses with more than two alleles to identify how sets of alleles,
genetically different strands at the same locus, have different response levels.
Plots show profiles over a chromosome.
Can handle multiple traits together.
See <https://github.com/byandell/qtl2pattern>.

Brian Yandell

qtl2pattern

Pattern Support for 'qtl2' Package

Brian S Yandell 

snpinfo_to_map function

<dl><dt>snpinfo</dt>
<dd>Data frame with SNP information with the following
 columns (the last three are generally derived from with
 <code>index_snps</code>):<ul>
<li><code>chr</code> - Character string or factor with chromosome</li>
<li><code>pos</code> - Position (in same units as in the <code>"map"</code>
 attribute in <code>genoprobs</code>.</li>
<li><code>sdp</code> - Strain distribution pattern: an integer, between
 1 and \(2^n - 2\) where \(n\) is the number of strains, whose
 binary encoding indicates the founder genotypes</li>
<li><code>snp</code> - Character string with SNP identifier (if
 missing, the rownames are used).</li>
<li><code>index</code> - Indices that indicate equivalent
 groups of SNPs.</li>
<li><code>intervals</code> - Indexes that indicate which marker
 intervals the SNPs reside.</li>
<li><code>on_map</code> - Indicate whether SNP coincides with a marker
 in the <code>genoprobs</code></li>
</ul></dd></dl>

Arguments

Convert SNP info to map — snpinfo_to_map

<dl>

<dt>snpinfo</dt>
<dd>Data frame with SNP information with the following
 columns (the last three are generally derived from with
 <code>index_snps</code>):<ul>
<li><code>chr</code> - Character string or factor with chromosome</li>
<li><code>pos</code> - Position (in same units as in the <code>"map"</code>
 attribute in <code>genoprobs</code>.</li>
<li><code>sdp</code> - Strain distribution pattern: an integer, between
 1 and \(2^n - 2\) where \(n\) is the number of strains, whose
 binary encoding indicates the founder genotypes</li>
<li><code>snp</code> - Character string with SNP identifier (if
 missing, the rownames are used).</li>
<li><code>index</code> - Indices that indicate equivalent
 groups of SNPs.</li>
<li><code>intervals</code> - Indexes that indicate which marker
 intervals the SNPs reside.</li>
<li><code>on_map</code> - Indicate whether SNP coincides with a marker
 in the <code>genoprobs</code></li>
</ul></dd>

</dl>

snpinfo_to_map: Convert SNP info to map

Description

Usage

Value

Arguments