A B C D F G I J L M N P R S T U V W
Achaz.stats | Class "GENOME" |
Achaz.stats-method | Achaz statistic |
Achaz.stats-methods | Achaz statistic |
BayeScanR | An R implementation of BayeScan (Foll & Gagiotti 2008) |
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 |
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 |
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) |
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 |
introgression.stats | Class "GENOME" |
introgression.stats-method | Introgression statistics |
introgression.stats-methods | Introgression statistics |
jack.knife.transform | Class "GENOME" |
jack.knife.transform-method | Jacknife Transformation |
jack.knife.transform-methods | Jacknife Transformation |
linkage.stats | Class "GENOME" |
linkage.stats-method | Linkage Disequilibrium |
linkage.stats-methods | Linkage Disequilibrium |
load.session | Loading a PopGenome session |
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 |
neutrality.stats | Class "GENOME" |
neutrality.stats-method | Neutrality Statistics |
neutrality.stats-methods | Neutrality Statistics |
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 |
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 |
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 |
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. |
usage-method | Class "GENOME" |
vcf_file | VCF file (subdirectory "data") |
VCF_split_into_scaffolds | Split a VCF file into multiple scaffold-VCFs |
weighted.jackknife | Class "GENOME" |
weighted.jackknife-method | Weighted Jackknife |
weighted.jackknife-methods | Weighted Jackknife |
Whop_readVCF | Reading tabixed VCF files (an interface to WhopGenome) |