missing_by_snp

This function can be run in two ways: 1) Without 'cutoff' specified. This will vizualise the
amount of missing data in each sample across a variety of potential missing data cutoffs.
Additionally, it will show you dotplots visualizing the number of total SNPs retained across
a variety of filtering cutoffs, and the total proportion of missing data.
Based on these visualizations, you can make an informed decision on what you think might be an
optimal cutoff to minimize the overall missingness of your dataset while still retaining an
appropriate amount of SNPs for the downstream inferences you hope to make 2) with 'cutoff'
specified. This option will show you the dotplots with the cutoff you set,
and then remove SNPs above the missing data cutoff.

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

missing_by_snp function

<dl><dt>vcfR</dt>
<dd>a vcfR object</dd>
<dt>cutoff</dt>
<dd>a numeric value between 0-1 specifying the maximum proportion of missing data
allowed in a SNP to be retained for downstream analyses</dd></dl>

Arguments

Vizualise missing data per SNP, remove SNPs above a missing data cutoff — missing_by_snp

<dl>

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


<dt>cutoff</dt>
<dd>a numeric value between 0-1 specifying the maximum proportion of missing data
allowed in a SNP to be retained for downstream analyses</dd>

</dl>

missing_by_snp: Vizualise missing data per SNP, remove SNPs above a missing data cutoff

Description

Usage

Value

Arguments

Examples