An Efficient Swiss Army Knife for Population Genomic Analyses


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Documentation for package ‘PopGenome’ version 2.2.3

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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
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 --

Whop_readVCF Reading tabixed VCF files (an interface to WhopGenome)