Man pages for PopGenome
An Efficient Swiss Army Knife for Population Genomic Analyses

Achaz.statsAchaz statistic
BayeScanRAn R implementation of BayeScan (Foll & Gagiotti 2008)
calc.fixed.shared-methodsFixed and shared polymorphisms
calc.R2-methodsLinkage statistics (R2, P-value, Distance)
codontablePrints the codon table which is used in the PopGenome...
concatenate.classesConcatenate GENOME classes
concatenate.regionsConcatenate regions
count.unknowns-methodsCalculate missing nucleotide frequencies
create.PopGenome.methodIntegration of own functions into the PopGenome-framework
detail.stats-methodsSeveral statistics
fasta_fileFASTA file (subdirectory "data")
F_ST.stats.2-methodsFixation Index (2)
F_ST.stats-methodsFixation Index
GENOME-classClass "GENOME"
getBayes-methodsGet values for BayeScanR
get.biallelic.matrix-methodsGet the biallelic matrix
get.codons-methodsDetailed information about the nature of codon changes
get.feature.namesFeature informations and GFF-attributes
get_gff_infoAnnotation info
get.individuals-methodsPrint the names/IDs of individuals
get.status-methodsState of calculations
gff_fileGFF file (subdirectory "data")
GFF_split_into_scaffoldsSplit a GFF file into multiple scaffold-GFFs
introgression.statsIntrogression statistics
jack.knife.transform-methodsJacknife Transformation
linkage.stats-methodsLinkage Disequilibrium
load.sessionLoading a PopGenome session
MKT-methodsMcDonald-Kreitman Test (McDonald & Kreitman 1991)
MSCoalescent simulation with or without selection
MS_getStatsGet the simulated MS/MSMS statistics
mult.linkage.statsMultilocus linkage statistics
neutrality.stats-methodsNeutrality Statistics
PG_plot.biallelic.matrixPlot the biallelic matrix
PopGplotSmoothed line-plot for multiple populations
read.big.fastaReading large FASTA alignments
readDataRead alignments and calculate summary data
readHapMapRead SNP data from the HapMap consortium
readMSRead output data from MS and MSMS
readSNPRead data in .SNP format
readVCFRead SNP data in tabixed VCF format
recomb.stats-methodsRecombination statistics a region and write it to a FASTA file
save.sessionSave the '"GENOME"' object of a PopGenome session
set.filter-methodsSetting filter to the analysis
set.outgroup-methodsDefine an outgroup
set.populations-methodsDefine populations
set.ref.positionsSet reference positions for SNP data
set.synnonsyn-methodsSet synonymous positions for SNP data
show.slots-methodsShow Slots of class GENOME
sliding.window.transform-methodsSliding Window Transformation
snp_file.SNP file (variant call data from 1001 Arabidopsis Genomes...
split_data_into_GFF_attributesSplit the data into GFF attributes
split_data_into_GFF_featuresSplit the data into GFF features data into subsites
sweeps.stats-methodsSelective Sweeps
test.params-classSet parameters for coalescent simulations with Hudson's MS...
vcf_fileVCF file (subdirectory "data")
VCF_split_into_scaffoldsSplit a VCF file into multiple scaffold-VCFs
weighted.jackknifeWeighted Jackknife
Whop_readVCFReading tabixed VCF files (an interface to WhopGenome)
PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.