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PopGenome (version 2.7.2)

An Efficient Swiss Army Knife for Population Genomic Analyses

Description

Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code.

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Version

Install

install.packages('PopGenome')

Monthly Downloads

302

Version

2.7.2

License

GPL-3

Maintainer

Bastian Pfeifer

Last Published

January 10th, 2020

Functions in PopGenome (2.7.2)

Achaz.stats-methods

Achaz statistic

F_ST.stats-methods

PG_plot.biallelic.matrix-methods

Plot the biallelic matrix

F_ST.stats.2-methods

Fixation Index (2)

Get the simulated MS/MSMS statistics

An R implementation of BayeScan (Foll \& Gagiotti 2008)

calc.R2-methods

Linkage statistics (R2, P-value, Distance)

McDonald-Kreitman Test (McDonald \& Kreitman 1991)

Coalescent simulation with or without selection

GFF_split_into_scaffolds

Split a GFF file into multiple scaffold-GFFs

Prints the codon table which is used in the PopGenome framework

concatenate.classes

Concatenate GENOME classes

get.codons-methods

Detailed information about the nature of codon changes

get.feature.names

Feature informations and GFF-attributes

calc.fixed.shared-methods

Fixed and shared polymorphisms

get.individuals-methods

Print the names/IDs of individuals

get.status-methods

State of calculations

Smoothed line-plot for multiple populations

concatenate.regions

Concatenate regions

Reading tabixed VCF files (an interface to WhopGenome)

VCF_split_into_scaffolds

Split a VCF file into multiple scaffold-VCFs

FASTA file (subdirectory "data")

count.unknowns-methods

Calculate missing nucleotide frequencies

create.PopGenome.method

Integration of own functions into the PopGenome-framework

diversity.stats-methods

linkage.stats-methods

Linkage Disequilibrium

jack.knife.transform

Jacknife Transformation

Read SNP data in tabixed VCF format

getBayes-methods

Get values for BayeScanR

Annotation info

recomb.stats-methods

Recombination statistics

Save the "GENOME" object of a PopGenome session

region.as.fasta-methods

Extract a region and write it to a FASTA file

get.biallelic.matrix-methods

Get the biallelic matrix

detail.stats-methods

Several statistics

set.synnonsyn-methods

Set synonymous positions for SNP data

introgression.stats-methods

Introgression statistics

set.filter-methods

Setting filter to the analysis

show.slots-methods

Show Slots of class GENOME

GFF file (subdirectory "data")

diversity.stats.between-methods

sliding.window.transform-methods

Sliding Window Transformation

.SNP file (variant call data from 1001 Arabidopsis Genomes project)

Loading a PopGenome session

Read alignments and calculate summary data

set.outgroup-methods

Define an outgroup

VCF file (subdirectory "data")

set.populations-methods

Define populations

Read SNP data from the HapMap consortium

test.params-class

Set parameters for coalescent simulations with Hudson's MS and Ewing's MSMS.

mult.linkage.stats-methods

Multilocus linkage statistics

set.ref.positions-methods

Set reference positions for SNP data

neutrality.stats-methods

Neutrality Statistics

split_data_into_GFF_attributes

Split the data into GFF attributes

Read output data from MS and MSMS

Read data in .SNP format

Reading large FASTA alignments

split_data_into_GFF_features

Split the data into GFF features

splitting.data-methods

Split data into subsites

weighted.jackknife-methods

Weighted Jackknife

sweeps.stats-methods

Selective Sweeps