ex_hapMatSmall_data

A subset of <code>ex_hapMat_data</code>, containing 10 sequences (haplotypes) with 20 SNVs.

datasets

Reconstructs perfect phylogeny at a user-given focal point and to depict and test association in a genomic region based on the reconstructed partitions. Charith B Karunarathna and Jinko Graham (2019) <bioRxiv:10.1101/674523>.

Charith Karunarathna

perfectphyloR

Reconstruct Perfect Phylogenies from DNA Sequence Data

ex_hapMatSmall_data function

A list of ten haplotypes with the physical positions of each SNV.<dl class="dl-horizontal">
<dt>hapmat</dt><dd>A matrix of 0's and 1's, with rows representing haplotypes and columns representing SNVs.</dd>
<dt>snvNames</dt><dd>A vector of names of SNVs for the columns of <code>hapmat</code>.</dd>
<dt>hapNames</dt><dd>A vector of names of haplotypes for the rows of <code>hapmat</code>.</dd>
<dt>posns</dt><dd>a numeric vector specifying the genomic positions (e.g. in base pairs) of SNVs in the
 columns of <code>hapmat</code>.</dd>
</dl>

Format

Example small dataset — ex_hapMatSmall_data

A list of ten haplotypes with the physical positions of each SNV.<dl class='dl-horizontal'>
<dt>hapmat</dt><dd>A matrix of 0's and 1's, with rows representing haplotypes and columns representing SNVs.</dd>
<dt>snvNames</dt><dd>A vector of names of SNVs for the columns of <code>hapmat</code>.</dd>
<dt>hapNames</dt><dd>A vector of names of haplotypes for the rows of <code>hapmat</code>.</dd>
<dt>posns</dt><dd>a numeric vector specifying the genomic positions (e.g. in base pairs) of SNVs in the
 columns of <code>hapmat</code>.</dd>
</dl>

ex_hapMatSmall_data: Example small dataset

Description

Usage

Arguments

Format