Summaries and Population Structure Analyses of Genetic Data

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) .

Description

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

Installation

To install the stable version from CRAN:

install.packages('strataG')

To install the latest version from GitHub:

# make sure you have Rtools installed
if (!require('devtools')) install.packages('devtools')
# install from GitHub
devtools::install_github('ericarcher/strataG', build_vignettes = TRUE)

Vignettes

# To see the list of available vignettes
browseVignettes("strataG") 
 
# To open a specific vignette
vignette("gtypes")

Creating and Manipulating gtypes Objects ( gtypes)
By-Locus Summaries ( summaries)
Working with sequences ( sequences)
Tests of Population Structure (population.structure)
Quality Assurance / Quality Control (qaqc)
Installing External Programs (external.programs)

Citation

The paper can be obtained here, and is cited as (preferred):

Archer, F. I., Adams, P. E. and Schneiders, B. B. (2016), strataG: An R package for manipulating, summarizing and analysing population genetic data. Mol Ecol Resour. doi:10.1111/1755-0998.12559

If desired, the current release version of the package can be cited as:

Archer, F. 2016. strataG: An R package for manipulating, summarizing and analysing population genetic data. R package version 1.0.6. Zenodo. http://doi.org/10.5281/zenodo.60416

Contact

submit suggestions and bug-reports: https://github.com/ericarcher/strataG/issues
send a pull request: https://github.com/ericarcher/strataG/
e-mail: [email protected]

version 2.0.2 (current on GitHub)

NOTE: In order to speed up indexing the data in large data sets, this version changes the underlying structure of the gtypes object by replacing the @loci data.frame slot with a @data data.table slot. The data.table has a id character column, a strata character column, and every column afterwards represents one locus. The @strata slot has been removed.
The loci accessor has been removed.
Added as.array which returns a 3-dimensional array with dimensions of [id, locus, allele].
The print (show) function for gtypes objects no longer shows a by-locus summary. The display was getting too slow for data sets with a large number of loci.
The summary function now includes by-sample results.
Fixed computational errors in population structure metrics due to incorrect sorting of stratification.
Added maf to return minimum allele frequency for each locus.
Added ldNe to calculate Ne.

version 1.0.6

Added read.arlequin back. Fixed missing function error with write.arlequin.
Added summarizeSamples
Changed evanno from base graphics to ggplot2
Updated logic in labelHaplotypes to assign haplotypes if possible alternative site combinations match a present haplotype
Added Zenodo DOI
Added shiny app (strataGUI) for creating gtypes objects, QA/QC, and population structure analyses
Added type argument to structurePlot to select between area and bar charts
Changed haplotypeLikelihoods to sequenceLikelihoods
neiDa now creates haplotypes before calculating metric
Fixed error in writePhase that was creating improper input files for PHASE

version 1.0.5

Fixed error in dupGenotypes, propSharedLoci, and propSharedIDs where missing genotypes were not being properly counted.
Added as.data.frame.gtypes.
Removed gtypes2df.
Added arguments to as.matrix.gtypes to include id and strata columns in output.
Removed the jmodeltest function as this functionality is available in the modeltest function in the phangorn package.
Added conversion functions gtypes2phyDat and phyDat2gtypes to facilitate interoperability with the phangorn package.
Removed read.arlequin.
Added alleleNames accessor for gtypes object, which returns list of allele names for each locus.