An efficient swiss army knife for population genetic & genomic analysis


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Documentation for package ‘PopGenome’ version 1.2.3

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A B C D F G L M N P R S T U

-- A --

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

-- B --

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

-- C --

concatenate_to_whole_genome Concatenate
create.PopGenome.method Integration of own functions in 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

-- F --

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.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.F_ST Class "GENOME"
get.F_ST-method Fixation Index
get.F_ST-methods Fixation Index
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 Reading alignments and calculating summary data
get.sum.data-methods Reading alignments and calculating 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

-- 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
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 --

popFSTN-method Class "GENOME"
PopGenome PopGenome
popGetBial Class "GENOME"
popGetBial-method Get the biallelic matrix
popGetBial-methods Get the biallelic matrix

-- R --

read.big.fasta Reading big FASTA alignments
readData Reading alignments and calculating summary data
readHapMap Reading SNP data from the HapMap consortium
readSNP Reading SNP data from the 1001 Genome-project
readVCF Reading SNP data from the 1000 Genome-project
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 as a FASTA file
region.as.fasta-methods Extract a region as a FASTA file

-- S --

save.session Saving a PopGenome-session
set.populations Class "GENOME"
set.populations-method Define populations
set.populations-methods Define populations
set.ref.positions Class "GENOME"
set.ref.positions-method Sets reference positions for SNP data
set.ref.positions-methods Sets reference positions for SNP data
set.synnonsyn Class "GENOME"
set.synnonsyn-method Sets synonymous positions for SNP data
set.synnonsyn-methods Sets 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.
splitting.data Class "GENOME"
splitting.data-method Splitting data into subsites
splitting.data-methods Splitting data into subsites
sweeps.stats Class "GENOME"
sweeps.stats-method Selective Sweeps
sweeps.stats-methods Selective Sweeps

-- T --

test.params Set parameter for Coalescent Simulation.
test.params-class Set parameter for Coalescent Simulation.

-- U --

usage-method Class "GENOME"