Learn R Programming
⚠️There's a newer version (2.4.905) of this package.Take me there.

strataG (version 1.0.3)

Summaries and Population Structure Analyses of Genetic Data

Description

A toolkit for analyzing stratified population genetic data.

Copy Link

Version

Install

install.packages('strataG')

Monthly Downloads

77

Version

1.0.3

License

GNU General Public License

Maintainer

Eric Archer

Last Published

April 4th, 2016

Functions in strataG (1.0.3)

createConsensus

Consensus Sequence
dolph.haps

Dolphin mtDNA Haplotype Sequences
as.matrix,gtypes-method

Convert gtypes To matrix
haplotypeLikelihoods

Haplotype Likelihoods
strataG-package

Summaries and population structure analyses of DNA sequence genotypic data
jmodeltest

jModelTest
fasta

Read and Write FASTA
dloop.g

Dolphin dLoop gtypes Object
sharedLoci

Shared Loci
removeSequences

Remove Sequences
TiTvRatio

Transition / Transversion Ratio
alleleSplit

Split Alleles For Diploid Data
freq2GenData

Convert Haplotype Frequency Matrices
summarizeSeqs

Sequence Summaries
df2gtypes

Convert a data.frame to gtypes
LDgenepop

Linkage Disequlibrium
bowhead.snps

Bowhead Whale SNP Genotypes
Hstats

Population structure statistics
gelato

GELATo - Group ExcLusion and Assignment Test
hweTest

Hardy-Weinberg Equilibrium
dupGenotypes

Duplicate Genotypes
mostDistantSequences

Most Distant Sequences
baseFreqs

Base Frequencies
strataSplit

Split Strata
nucleotideDiversity

Nucleotide Diversity
tajimasD

Tajima's D
gtypes2df

Convert gtypes To data.frame
heterozygosity

Observed and Expected Heterozygosity
labelHaplotypes

Find and label haplotypes
iupacCode

IUPAC Code
neiDa

Nei's Da
dolph.strata

Dolphin Genetic Stratification and Haplotypes
msats.g

Dolphin Microsatellite gtypes Object
wrightFst

Wright's Fst
lowFreqSubs

Low Frequency Substitutions
show,gtypes-method

Show a gtypes object
mRatio

M ratio
numGensEq

Number of Generations to Equilibrium
nucleotideDivergence

Nucleotide Divergence
evanno

Run Evanno Method on STRUCTURE Results
popStructTest

Population Differentiation Tests
phase

PHASE
sequence2gtypes

Convert Sequences To gtypes
trimNs

Trim N's From Sequences
exptdNumAlleles

Expected Number of Alleles
write.gtypes

Write gtypes
fixedSites

Fixed Sites
parseLocusNames

Parse Locus Names
mostRepresentativeSequences

Representative Sequences
validIupacCodes

Valid IUPAC Codes
structurePlot

Plot STRUCTURE Results
fusFs

Fu's Fs
permuteStrata

Permute strata
stratify

Stratify gtypes
genepop

Run GENEPOP
gtypes-class

gtypes Class
arlequin

Read and Write Arlequin Files
gtypes2loci

Convert Between gtypes And loci objects.
mafft

MAFFT Alignment
fastsimcoal.input

Input functions for fastsimcoal parameters
privateAlleles

Private Alleles
variableSites

Variable Sites
theta

Theta
structure

STRUCTURE
propUniqueAlleles

Proportion Unique Alleles
allelicRichness

Allelic Richness
numMissing

Number Missing Data
summarizeLoci

Locus Summaries
qaqc

Quality Assurance/Quality Control
mega

Read and Write MEGA
clumpp

Run CLUMPP
gtypes.accessors

gtypes Accessors
readGenData

Read Genetic Data
jackHWE

Hardy-Weinberg Equlibrium Jackknife
alleleFreqFormat

Compiles and Formats Allele Frequencies
write.nexus.snapp

Write NEXUS File for SNAPP
fstToNm

Nm from Fst
bowhead.snp.position

Bowhead Whale SNP Genotype Groups
gtypes2genind

Convert Between gtypes And genind objects.
dolph.seqs

Dolphin mtDNA D-loop Sequences
fixedDifferences

Fixed Differences
numAlleles

Number of Alleles
initialize,gtypes-method

gtypes Constructor
idRows

gtypes ID Rows
fastsimcoal

Run fastsimcoal
as.multidna

Convert to multidna
simGammaHaps

Simulate Haplotypes
summary,gtypes-method

Summarize gtypes Object
alleleFreqs

Allele Frequencies
dolph.msats

Dolphin Microsatellite Genotypes