strataG (version 1.0.3)

qaqc: Quality Assurance/Quality Control

Description

Conducts a suite of QA/QC tests. Summarizes missing data and homozygosity by individual and locus, and looks for duplicate genotypes (see dupGenotypes). For sequence data, identifies low frequency substitutions (see lowFreqSubs), and computes haplotype likelihoods (see haplotypeLikelihoods).

Usage

qaqc(g, label = NULL, ...)

Arguments

g

a gtypes object.

label

optional label for output folder and prefix for files.

...

optional arguments to pass on to summary functions.

Value

• Files are written for by-sample and by-locus summaries, and duplicate genotypes if any are found. If sequences are present, files are written identifying low frequency substitutions and haplotype likelihoods. The return value is a list with the following elements: ll{ by.sample data.frame of by-sample summaries. by.locus data.frame of by-locus summaries. dup.df data.frame identifying potential duplicates. by.seq list of low frequency substitutions and haplotype likelihoods for each gene. }