Achaz.stats | Class "GENOME" |
Achaz.stats-method | Achaz statistic |
Achaz.stats-methods | Achaz statistic |
BayeScanR | An R-version of BayeScan (Foll & Gagiotti 2008) |
concatenate_to_whole_genome | Concatenate |
create.PopGenome.method | Integration of own functions in 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 |
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.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 |
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 |
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 |
popFSTN-method | Class "GENOME" |
PopGenome | PopGenome |
popGetBial | Class "GENOME" |
popGetBial-method | Get the biallelic matrix |
popGetBial-methods | Get the biallelic matrix |
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 |
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 |
test.params | Set parameter for Coalescent Simulation. |
test.params-class | Set parameter for Coalescent Simulation. |
usage-method | Class "GENOME" |