Locus

Locus-class

This is a S4 <code>Locus</code> classs for a marker (e.g., SNP) locus.

Applies a unified local function to select SNPs for low-density
SNPs. The method is described in Wu et al. (2020) <doi:10.1111/age.12916>.
Briefly, the local function gives different weights to the uniformity (U score)
and average Shannon entropy (E score), depending on the inputs of the weights,
thus facilitating SNP designs under varied scenarios for low-density SNP chips,
including selecting uniformly-distributed SNPs or SNPs with the highest minor
allele frequencies. This is an educational version. For more information about
this package, please contact Dr. Nick Wu.

Nick Wu

selectSNPs

Optimal Selection of SNPs Using a Unified Local Function

Locus function

<dl class="dl-horizontal">
 <dt><code>Name</code>:</dt><dd>A character string as the name of this marker locus.</dd>
 <dt><code>Chromosome</code>:</dt><dd>A character string as the name of the chromosome for this marker.</dd>
 <dt><code>Position</code>:</dt><dd>A numeric number as the chromosomal position of this marker.</dd>
 <dt><code>Maf</code>:</dt><dd>A numeric number for the minor allele frquency at this locus.</dd>
 <dt><code>Type</code>:</dt><dd>A character specifying the type of this locus, which can be "A", "B", or "C".
 The default value is "C" when the input is missing.</dd>
 <dt><code>Status</code>:</dt><dd>A integer specifying the status of tihs locus, wihch can be 1 for obligatory
 markers or 0 otherwise. The default value is 0 when missing the input.</dd>
 </dl>

Locus: The Locus class

Description

Arguments

Slots

Details