Man pages for PopGenome
An Efficient Swiss Army Knife for Population Genomic Analyses
| Achaz.stats | Achaz statistic |
| BayeScanR | An R implementation of BayeScan (Foll & Gagiotti 2008) |
| calc.fixed.shared-methods | Fixed and shared polymorphisms |
| calc.R2-methods | Linkage statistics (R2, P-value, Distance) |
| codontable | Prints the codon table which is used in the PopGenome... |
| concatenate.classes | Concatenate GENOME classes |
| concatenate.regions | Concatenate regions |
| count.unknowns-methods | Calculate missing nucleotide frequencies |
| create.PopGenome.method | Integration of own functions into the PopGenome-framework |
| detail.stats-methods | Several statistics |
| diversity.stats.between-methods | Diversities |
| diversity.stats-methods | Diversities |
| fasta_file | FASTA file (subdirectory "data") |
| F_ST.stats.2-methods | Fixation Index (2) |
| F_ST.stats-methods | Fixation Index |
| GENOME-class | Class "GENOME" |
| getBayes-methods | Get values for BayeScanR |
| get.biallelic.matrix-methods | Get the biallelic matrix |
| get.codons-methods | Detailed information about the nature of codon changes |
| get.feature.names | Feature informations and GFF-attributes |
| get_gff_info | Annotation info |
| get.individuals-methods | Print the names/IDs of individuals |
| get.status-methods | State of calculations |
| gff_file | GFF file (subdirectory "data") |
| GFF_split_into_scaffolds | Split a GFF file into multiple scaffold-GFFs |
| introgression.stats | Introgression statistics |
| jack.knife.transform-methods | Jacknife Transformation |
| linkage.stats-methods | Linkage Disequilibrium |
| load.session | Loading a PopGenome session |
| 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 | Multilocus linkage statistics |
| neutrality.stats-methods | Neutrality Statistics |
| PG_plot.biallelic.matrix | Plot the biallelic matrix |
| PopGenome | PopGenome |
| PopGplot | Smoothed line-plot for multiple populations |
| 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-methods | Recombination statistics |
| region.as.fasta | Extract a region and write it to a FASTA file |
| save.session | Save the '"GENOME"' object of a PopGenome session |
| set.filter-methods | Setting filter to the analysis |
| set.outgroup-methods | Define an outgroup |
| set.populations-methods | Define populations |
| set.ref.positions | Set reference positions for SNP data |
| set.synnonsyn-methods | Set synonymous positions for SNP data |
| show.slots-methods | Show Slots of class GENOME |
| sliding.window.transform-methods | Sliding Window Transformation |
| snp_file | .SNP file (variant call data from 1001 Arabidopsis Genomes... |
| split_data_into_GFF_attributes | Split the data into GFF attributes |
| split_data_into_GFF_features | Split the data into GFF features |
| splitting.data-methods | Split data into subsites |
| sweeps.stats-methods | Selective Sweeps |
| test.params-class | Set parameters for coalescent simulations with Hudson's MS... |
| vcf_file | VCF file (subdirectory "data") |
| VCF_split_into_scaffolds | Split a VCF file into multiple scaffold-VCFs |
| weighted.jackknife | Weighted Jackknife |
| Whop_readVCF | Reading tabixed VCF files (an interface to WhopGenome) |
