distance_thin

This function requires a vcfR object as input, and returns a vcfR object filtered
to retain only SNPs greater than a specified distance apart on each scaffold.
The function starts by automatically retaining the first SNP on a given scaffold,
and then subsequently keeping the next SNP that is greater than the specified distance away,
until it reaches the end of the scaffold/chromosome. This function scales well with
an increasing number of SNPs, but poorly with an increasing number of scaffolds/chromosomes.
For this reason, there is a built in progress bar,
to monitor potentially long-running executions with many scaffolds.
This type of filtering is often employed to reduce linkage among input SNPs,
especially for downstream input to programs like structure, which require unlinked SNPs.

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

distance_thin function

<dl><dt>vcfR</dt>
<dd>a vcfR object</dd>
<dt>min.distance</dt>
<dd>a numeric value representing the smallest distance (in base-pairs)
allowed between SNPs after distance thinning</dd></dl>

Arguments

Filter a vcf file based on distance between SNPs on a given scaffold — distance_thin

<dl>

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


<dt>min.distance</dt>
<dd>a numeric value representing the smallest distance (in base-pairs)
allowed between SNPs after distance thinning</dd>

</dl>

distance_thin: Filter a vcf file based on distance between SNPs on a given scaffold

Description

Usage

Value

Arguments

Examples