# An Efficient Swiss Army Knife for Population Genomic Analyses

## Documentation for package ‘PopGenome’ version 2.7.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G I J L M N P R S T U V W

## -- A --

Achaz.stats | Class "GENOME"
Achaz.stats-method | Achaz statistic
Achaz.stats-methods | Achaz statistic

## -- B --

BayeScanR | An R implementation of BayeScan (Foll & Gagiotti 2008)

## -- C --

calc.fixed.shared | Class "GENOME"
calc.fixed.shared-method | Fixed and shared polymorphisms
calc.fixed.shared-methods | Fixed and shared polymorphisms
calc.R2 | Class "GENOME"
calc.R2-method | Linkage statistics (R2, P-value, Distance)
calc.R2-methods | Linkage statistics (R2, P-value, Distance)
codontable | Prints the codon table which is used in the PopGenome framework
concatenate.classes | Concatenate GENOME classes
concatenate.regions | Concatenate regions
count.unknowns | Class "GENOME"
count.unknowns-method | Calculate missing nucleotide frequencies
count.unknowns-methods | Calculate missing nucleotide frequencies
create.PopGenome.method | Integration of own functions into the PopGenome-framework

## -- D --

detail.stats | Class "GENOME"
detail.stats-method | Several statistics
detail.stats-methods | Several statistics
diversity.stats | Class "GENOME"
diversity.stats-method | Diversities
diversity.stats-methods | Diversities
diversity.stats.between | Class "GENOME"
diversity.stats.between-method | Diversities
diversity.stats.between-methods | Diversities

## -- F --

fasta_file | FASTA file (subdirectory "data")
F_ST.stats | Class "GENOME"
F_ST.stats-method | Fixation Index
F_ST.stats-methods | Fixation Index
F_ST.stats.2 | Class "GENOME"
F_ST.stats.2-method | Fixation Index (2)
F_ST.stats.2-methods | Fixation Index (2)

## -- G --

GENOME-class | Class "GENOME"
get.biallelic.matrix | Class "GENOME"
get.biallelic.matrix-method | Get the biallelic matrix
get.biallelic.matrix-methods | Get the biallelic matrix
get.codons | Class "GENOME"
get.codons-method | Detailed information about the nature of codon changes
get.codons-methods | Detailed information about the nature of codon changes
get.detail | Class "GENOME"
get.detail-method | Several statistics
get.detail-methods | Several statistics
get.diversity | Class "GENOME"
get.diversity-method | Fixation Index
get.diversity-methods | Fixation Index
get.feature.names | Feature informations and GFF-attributes
get.F_ST | Class "GENOME"
get.F_ST-method | Fixation Index
get.F_ST-methods | Fixation Index
get.individuals | Class "GENOME"
get.individuals-method | Print the names/IDs of individuals
get.individuals-methods | Print the names/IDs of individuals
get.linkage | Class "GENOME"
get.linkage-method | Linkage Disequilibrium
get.linkage-methods | Linkage Disequilibrium
get.MKT | Class "GENOME"
get.MKT-method | McDonald-Kreitman Test (McDonald & Kreitman 1991)
get.MKT-methods | McDonald-Kreitman Test (McDonald & Kreitman 1991)
get.neutrality | Class "GENOME"
get.neutrality-method | Neutrality Statistics
get.neutrality-methods | Neutrality Statistics
get.recomb | Class "GENOME"
get.recomb-method | Recombination statistics
get.recomb-methods | Recombination statistics
get.status | Class "GENOME"
get.status-method | State of calculations
get.status-methods | State of calculations
get.sum.data | Class "GENOME"
get.sum.data-method | Read alignments and calculate summary data
get.sum.data-methods | Read alignments and calculate summary data
get.sweeps | Class "GENOME"
get.sweeps-method | Selective Sweeps
get.sweeps-methods | Selective Sweeps
getBayes | Class "GENOME"
getBayes-method | Get values for BayeScanR
getBayes-methods | Get values for BayeScanR
getMS-method | Class "GENOME"
get_gff_info | Annotation info
gff_file | GFF file (subdirectory "data")
GFF_split_into_scaffolds | Split a GFF file into multiple scaffold-GFFs

## -- I --

introgression.stats | Class "GENOME"
introgression.stats-method | Introgression statistics
introgression.stats-methods | Introgression statistics

## -- J --

jack.knife.transform | Class "GENOME"
jack.knife.transform-method | Jacknife Transformation
jack.knife.transform-methods | Jacknife Transformation

## -- L --

linkage.stats | Class "GENOME"
linkage.stats-method | Linkage Disequilibrium
linkage.stats-methods | Linkage Disequilibrium
load.session | Loading a PopGenome session

## -- M --

MKT | Class "GENOME"
MKT-method | McDonald-Kreitman Test (McDonald & Kreitman 1991)
MKT-methods | McDonald-Kreitman Test (McDonald & Kreitman 1991)
MS | Coalescent simulation with or without selection
MS_getStats | Get the simulated MS/MSMS statistics
mult.linkage.stats | Class "GENOME"
mult.linkage.stats-method | Multilocus linkage statistics
mult.linkage.stats-methods | Multilocus linkage statistics

## -- N --

neutrality.stats | Class "GENOME"
neutrality.stats-method | Neutrality Statistics
neutrality.stats-methods | Neutrality Statistics

## -- P --

PG_plot.biallelic.matrix | Class "GENOME"
PG_plot.biallelic.matrix-method | Plot the biallelic matrix
PG_plot.biallelic.matrix-methods | Plot the biallelic matrix
popFSTN-method | Class "GENOME"
PopGenome | PopGenome
PopGplot | Smoothed line-plot for multiple populations

## -- R --

read.big.fasta | Reading large FASTA alignments
readData | Read alignments and calculate summary data
readHapMap | Read SNP data from the HapMap consortium
readMS | Read output data from MS and MSMS
readSNP | Read data in .SNP format
readVCF | Read SNP data in tabixed VCF format
recomb.stats | Class "GENOME"
recomb.stats-method | Recombination statistics
recomb.stats-methods | Recombination statistics
region.as.fasta | Class "GENOME"
region.as.fasta-method | Extract a region and write it to a FASTA file
region.as.fasta-methods | Extract a region and write it to a FASTA file

## -- S --

save.session | Save the '"GENOME"' object of a PopGenome session
set.filter | Class "GENOME"
set.filter-method | Setting filter to the analysis
set.filter-methods | Setting filter to the analysis
set.outgroup | Class "GENOME"
set.outgroup-method | Define an outgroup
set.outgroup-methods | Define an outgroup
set.populations | Class "GENOME"
set.populations-method | Define populations
set.populations-methods | Define populations
set.ref.positions | Class "GENOME"
set.ref.positions-method | Set reference positions for SNP data
set.ref.positions-methods | Set reference positions for SNP data
set.synnonsyn | Class "GENOME"
set.synnonsyn-method | Set synonymous positions for SNP data
set.synnonsyn-methods | Set synonymous positions for SNP data
show-method | Class "GENOME"
show.slots | Class "GENOME"
show.slots-method | Show Slots of class GENOME
show.slots-methods | Show Slots of class GENOME
sliding.window.transform | Class "GENOME"
sliding.window.transform-method | Sliding Window Transformation
sliding.window.transform-methods | Sliding Window Transformation
snp_file | .SNP file (variant call data from 1001 Arabidopsis Genomes project)
splitting.data | Class "GENOME"
splitting.data-method | Split data into subsites
splitting.data-methods | Split data into subsites
split_data_into_GFF_attributes | Split the data into GFF attributes
split_data_into_GFF_features | Split the data into GFF features
sweeps.stats | Class "GENOME"
sweeps.stats-method | Selective Sweeps
sweeps.stats-methods | Selective Sweeps

## -- T --

test.params | Set parameters for coalescent simulations with Hudson's MS and Ewing's MSMS.
test.params-class | Set parameters for coalescent simulations with Hudson's MS and Ewing's MSMS.

## -- U --

usage-method | Class "GENOME"

## -- V --

vcf_file | VCF file (subdirectory "data")
VCF_split_into_scaffolds | Split a VCF file into multiple scaffold-VCFs

## -- W --

weighted.jackknife | Class "GENOME"
weighted.jackknife-method | Weighted Jackknife
weighted.jackknife-methods | Weighted Jackknife
Whop_readVCF | Reading tabixed VCF files (an interface to WhopGenome)