A function to remove the alleles with minimum allele frequency and keep only
a bi-allelic matrix when loci are multi-allelic

Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).

Piyal Karunarathne

rCNV

Detect Copy Number Variants from SNPs Data

Qiujie Zhou

Klaus Schliep

Pascal Milesi

maf function

<dl><dt>h.table</dt>
<dd>allele depth table generated from the function <code>hetTgen</code></dd>
<dt>AD</dt>
<dd>logical. If TRUE a allele depth table similar to <code>hetTgen</code>
output will be returns; If <code>FALSE</code>, individual AD values per SNP will be
returned in a list.</dd>
<dt>verbose</dt>
<dd>logical. Show progress</dd>
<dt>parallel</dt>
<dd>logical. whether to parallelize the process</dd></dl>

Arguments

Author

Remove MAF allele — maf

<dl>

<dt>h.table</dt>
<dd>allele depth table generated from the function <code>hetTgen</code></dd>


<dt>AD</dt>
<dd>logical. If TRUE a allele depth table similar to <code>hetTgen</code>
output will be returns; If <code>FALSE</code>, individual AD values per SNP will be
returned in a list.</dd>


<dt>verbose</dt>
<dd>logical. Show progress</dd>


<dt>parallel</dt>
<dd>logical. whether to parallelize the process</dd>

</dl>

maf: Remove MAF allele

Description

Usage

Value

Arguments

Author

Examples