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PopGenome (version 1.2.6)

A swiss army knife for population genetic & genomic analysis

Description

PopGenome is an R-package for Population Genetic & Genomic Analysis

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Version

Install

install.packages('PopGenome')

Monthly Downloads

83

Version

1.2.6

License

GPL-3

Maintainer

Bastian Pfeifer

Last Published

November 17th, 2013

Functions in PopGenome (1.2.6)

mult.linkage.stats-methods

Multilocus linkage statistics
F_ST.stats-methods

Fixation Index
diversity.stats-methods

Diversities
gff_file

GFF file (subdirectory "data")
PopGenome

PopGenome
detail.stats-methods

Several statistics
get.individuals-methods

Print the individual names
set.populations-methods

Define populations
splitting.data-methods

Splitting data into subsites
readSNP

Reading SNP data from the 1001 Genome-project
Achaz.stats-methods

Achaz statistic
get.status-methods

State of Calculations
fasta_file

FASTA file (subdirectory "data")
concatenate.regions

Concatenate regions
readVCF

Reading SNP data from the 1000 Genome-project
recomb.stats-methods

Recombination statistics
set.synnonsyn-methods

Sets synonymous positions for SNP data
F_ST.stats.2-methods

Fixation Index (2)
GENOME-class

Class "GENOME"
getBayes-methods

Get values for BayeScanR
test.params-class

Set parameter for Coalescent Simulation.
save.session

Saving a PopGenome-session
set.ref.positions-methods

Sets reference positions for SNP data
MKT-methods

McDonald-Kreitman Test (McDonald & Kreitman 1991)
neutrality.stats-methods

Neutrality Statistics
vcf_file

VCF file (subdirectory "data")
readHapMap

Reading SNP data from the HapMap consortium
set.outgroup-methods

Define an outgroup
region.as.fasta-methods

Extract a region as a FASTA file
BayeScanR

An R-version of BayeScan (Foll & Gagiotti 2008)
get_gff_info

Annotation info
show.slots-methods

Show Slots of class GENOME
snp_file

SNP file (variant call (1001 Genome project)
get.codons-methods

Detail informations about codon-substitutions
MS

Coalescent Simulation with or without selection
create.PopGenome.method

Integration of own functions in the PopGenome-framework
load.session

Loading a PopGenome-session
readMS

Reading data from MS and MSMS output
read.big.fasta

Reading big FASTA alignments
calc.R2-methods

Linkage statistics (R2, P-value, Distance)
PG_plot.biallelic.matrix-methods

Plots the Biallelic Matrix
get.biallelic.matrix-methods

Get the biallelic matrix
readData

Reading alignments and calculating summary data
sweeps.stats-methods

Selective Sweeps
concatenate.classes

Concatenate GENOME classes
linkage.stats-methods

Linkage Disequilibrium
sliding.window.transform-methods

Sliding Window Transformation.