qaqc

a <a href="/link/?package=strataG&version=2.0.2" gtypes'="" data-mini-rdoc="strataG::"></a>'>gtypes object.

optional label for output folder and prefix for files.

label

optional arguments to pass on to summary functions.

Conducts a suite of QA/QC tests. Summarizes missing data and 
 homozygosity by individual and locus, and looks for duplicate genotypes 
 (see <code><a rd-options="" href="/link/dupGenotypes?package=strataG&version=2.0.2" data-mini-rdoc="strataG::dupGenotypes">dupGenotypes</a></code>). For sequence data, identifies low 
 frequency substitutions (see <code><a rd-options="" href="/link/lowFreqSubs?package=strataG&version=2.0.2" data-mini-rdoc="strataG::lowFreqSubs">lowFreqSubs</a></code>), and computes 
 sequence likelihoods (see <code><a rd-options="" href="/link/sequenceLikelihoods?package=strataG&version=2.0.2" data-mini-rdoc="strataG::sequenceLikelihoods">sequenceLikelihoods</a></code>).

A toolkit for analyzing stratified population genetic data.
Functions are provided for summarizing and checking loci
(haploid, diploid, and polyploid), single stranded DNA sequences,
calculating most population subdivision metrics, and running external programs
such as structure and fastsimcoal. The package is further described in
Archer et al (2016) <doi:10.1111/1755-0998.12559>.

Eric Archer

strataG

Summaries and Population Structure Analyses of Genetic Data

Brita Schneiders

Paula Adams

Sarina Fernandez

Warren Asfazadour

qaqc function

a <a href='<a href='gtypes'></a>'>gtypes</a> object.

Conducts a suite of QA/QC tests. Summarizes missing data and 
 homozygosity by individual and locus, and looks for duplicate genotypes 
 (see <code><a rd-options='' href='dupGenotypes'>dupGenotypes</a></code>). For sequence data, identifies low 
 frequency substitutions (see <code><a rd-options='' href='lowFreqSubs'>lowFreqSubs</a></code>), and computes 
 sequence likelihoods (see <code><a rd-options='' href='sequenceLikelihoods'>sequenceLikelihoods</a></code>).

qaqc: Quality Assurance/Quality Control

Description

Usage

Arguments

Value

See Also