Chrom

Chrom-class

This is a S4 <code>Chrom</code> classs for a single chromosome

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

Chrom function

<dl class="dl-horizontal">
 <dt><code>Chromosome</code>:</dt><dd>A character string as the chromosome name or index.</dd>
 <dt><code>Name</code>:</dt><dd>A character vector containing the names for all the markers on this chromosome.</dd>
 <dt><code>Position</code>:</dt><dd>A numeric vector containing the positions of all the markers on this chromosome.</dd>
 <dt><code>Maf</code>:</dt><dd>A numeric vector containing the minor allele frequencies of all the markers on
 this chromosome.</dd>
 <dt><code>Type</code>:</dt><dd>A character vector containing the types for all the markers on this chromosome.</dd>
 <dt><code>Status</code>:</dt><dd>An integer vector containing the statuses for all the markers on this chromosome.</dd>
 </dl>

Chrom: The Chromosome class

Description

Arguments

Slots

Details