filter_allele_balance

This function requires a vcfR object as input, and returns a vcfR object filtered
to convert heterozygous sites with an allele balance falling outside of the
specified ratio to 'NA'. If no ratio is specified, a default .25-.75 limit is imposed.
From the <a href="https://www.ddocent.com/filtering/">dDocent filtering page</a> "Allele balance:
a number between 0 and 1 representing the ratio of reads showing the reference allele to
all reads, considering only reads from individuals called as heterozygous, we expect that the
allele balance in our data (for real loci) should be close to 0.5".

Is designed to interactively and reproducibly visualize and filter SNP
(single-nucleotide polymorphism) datasets. This R-based implementation of SNP
and genotype filters facilitates
an interactive and iterative SNP filtering pipeline, which can be documented
reproducibly via Rmarkdown. 'SNPfiltR' contains functions for visualizing
various quality and missing data metrics for a SNP dataset, and then filtering
the dataset based on user specified cutoffs.
All functions take 'vcfR' objects as input, which can easily be
generated by reading standard vcf (variant call format) files into R using
the R package 'vcfR' (Knaus and Grünwald) (<doi:10.1111/1755-0998.12549>).
Each 'SNPfiltR' function can return a newly filtered vcfR object, which can then be
written to a local directory in standard vcf format using the 'vcfR' package,
for downstream population genetic and phylogenetic analyses.

Devon DeRaad

SNPfiltR

Interactively Filter SNP Datasets

filter_allele_balance function

<dl><dt>vcfR</dt>
<dd>a vcfR object</dd>
<dt>min.ratio</dt>
<dd>minumum allele ratio for a called het</dd>
<dt>max.ratio</dt>
<dd>maximum allele ratio for a called het</dd></dl>

Arguments

This function requires a vcfR object as input, and returns a vcfR object filtered
to convert heterozygous sites with an allele balance falling outside of the
specified ratio to 'NA'. If no ratio is specified, a default .25-.75 limit is imposed.
From the <a href='https://www.ddocent.com/filtering/'>dDocent filtering page</a> "Allele balance:
a number between 0 and 1 representing the ratio of reads showing the reference allele to
all reads, considering only reads from individuals called as heterozygous, we expect that the
allele balance in our data (for real loci) should be close to 0.5".

Filter out heterozygous genotypes failing an allele balance check — filter_allele_balance

<dl>

<dt>vcfR</dt>
<dd>a vcfR object</dd>


<dt>min.ratio</dt>
<dd>minumum allele ratio for a called het</dd>


<dt>max.ratio</dt>
<dd>maximum allele ratio for a called het</dd>

</dl>

filter_allele_balance: Filter out heterozygous genotypes failing an allele balance check

Description

Usage

Value

Arguments

Examples