Learn R Programming

⚠️There's a newer version (2.7.5) of this package.Take me there.

PopGenome (version 2.1.6)

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.

Copy Link

Version

Install

install.packages('PopGenome')

Monthly Downloads

119

Version

2.1.6

License

GPL-3

Maintainer

Bastian Pfeifer

Last Published

May 4th, 2015

Functions in PopGenome (2.1.6)

diversity.stats-methods

Coalescent simulation with or without selection

Prints the codon table which is used in the PopGenome framework

PG_plot.biallelic.matrix-methods

Plot the biallelic matrix

count.unknowns-methods

Calculate missing nucleotide frequencies

Loading a PopGenome session

Reading large FASTA alignments

recomb.stats-methods

Recombination statistics

sliding.window.transform-methods

Sliding Window Transformation

set.synnonsyn-methods

Set synonymous positions for SNP data

Read output data from MS and MSMS

set.outgroup-methods

Define an outgroup

VCF_split_into_scaffolds

Split a VCF file into multiple scaffold-VCFs

concatenate.regions

Concatenate regions

Read data in .SNP format

create.PopGenome.method

Integration of own functions into the PopGenome-framework

McDonald-Kreitman Test (McDonald & Kreitman 1991)

detail.stats-methods

Several statistics

F_ST.stats.2-methods

Fixation Index (2)

sweeps.stats-methods

Selective Sweeps

F_ST.stats-methods

test.params-class

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

Reading tabixed VCF files (an interface to WhopGenome)

set.ref.positions-methods

Set reference positions for SNP data

get.codons-methods

Detailed information about the nature of codon changes

GFF_split_into_scaffolds

Split a GFF file into multiple scaffold-GFFs

linkage.stats-methods

Linkage Disequilibrium

FASTA file (subdirectory "data")

Save the "GENOME" object of a PopGenome session

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

set.populations-methods

Define populations

introgression.stats-methods

Introgression statistics

An R implementation of BayeScan (Foll & Gagiotti 2008)

get.biallelic.matrix-methods

Get the biallelic matrix

VCF file (subdirectory "data")

Read alignments and calculate summary data

Annotation info

concatenate.classes

Concatenate GENOME classes

get.status-methods

State of calculations

get.individuals-methods

Print the names/IDs of individuals

mult.linkage.stats-methods

Multilocus linkage statistics

neutrality.stats-methods

Neutrality Statistics

GFF file (subdirectory "data")

Read SNP data from the HapMap consortium

region.as.fasta-methods

Extract a region and write it to a FASTA file

splitting.data-methods

Split data into subsites

Achaz.stats-methods

Achaz statistic

calc.R2-methods

Linkage statistics (R2, P-value, Distance)

getBayes-methods

Get values for BayeScanR

split_data_into_GFF_attributes

Split the data into GFF attributes

Read SNP data in tabixed VCF format

Smoothed line-plot for multiple populations

get.feature.names

Feature informations and GFF-attributes

show.slots-methods

Show Slots of class GENOME

jack.knife.transform

Jacknife Transformation

Get the simulated MS/MSMS statistics