Man pages for poolfstat
Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data
| add.leaf | Test all possible connection of a leaf to a graph with... |
| bjack_cov | bjack_cov |
| block_sum | block_sum |
| block_sum2 | block_sum2 |
| compare.fitted.fstats | Compare fitted f2, f3 and f4 f-statistics of an admixture... |
| compute_blockDdenom | compute_blockDdenom |
| compute_F3fromF2 | compute_F3fromF2 |
| compute_F3fromF2samples | compute_F3fromF2samples |
| compute_F4DfromF2samples | compute_F4DfromF2samples |
| compute_F4fromF2 | compute_F4fromF2 |
| compute_F4fromF2samples | compute_F4fromF2samples |
| compute.f4ratio | Compute F4ratio (estimation of admixture rate) from an fstats... |
| computeFST | Compute Fst from Pool-Seq data or Count data |
| compute.fstats | Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and... |
| compute_H1 | compute_H1 |
| compute.pairwiseFST | Compute pairwise population population FST matrix (and... |
| compute_Q2 | compute_Q2 |
| compute_QmatfromF2samples | compute_QmatfromF2samples |
| compute_snpFstAov | compute_snpFstAov |
| compute_snpHierFstAov | compute_snpHierFstAov |
| compute_snpQ1 | compute_snpQ1 |
| compute_snpQ1onepop | compute_snpQ1onepop |
| compute_snpQ1rw | compute_snpQ1rw |
| compute_snpQ2 | compute_snpQ2 |
| compute_snpQ2onepair | compute_snpQ2onepair |
| compute_snpQ2w | compute_snpQ2rw |
| countdata2genobaypass | Convert a countdata object into BayPass input files. |
| countdata-class | S4 class to represent a Count data set. |
| countdata.subset | Create a subset of a countdata object that contains count... |
| extract_allele_names | extract_allele_names |
| extract_nonvscan_counts | extract_nonvscan_counts |
| extract_vscan_counts | extract_vscan_counts |
| find_indelneighbor_idx | find_indelneighbor_idx |
| find.tree.popset | Find sets of populations that may used as scaffold tree |
| fit.graph | Estimate parameters of an admixture graph |
| fitted.graph-class | S4 class to represent a population tree or admixture graph... |
| fstats-class | S4 class to represent fstats results obtained with... |
| generateF3names | generateF3names |
| generateF4names | generateF4names |
| generate.graph.params | Generate a graph parameter object to fit admixture graph to... |
| generate.jackknife.blocks | Generate block coordinates for block-jackknife |
| genobaypass2countdata | Convert BayPass allele count input files into a coundata... |
| genobaypass2pooldata | Convert BayPass read count and haploid pool size input files... |
| genoselestim2pooldata | Convert SelEstim read count input files into a pooldata... |
| genotreemix2countdata | Convert allele count input files from the Treemix program... |
| graph.builder | Implement a graph builder heuristic by successively adding... |
| graph.params2qpGraphFiles | Generate files for the qpGraph software from a graph.params... |
| graph.params2symbolic.fstats | Provide a symbolic representation of all the F-statistics and... |
| graph.params-class | S4 class to represent a population tree or admixture graph... |
| heatmap-pairwisefst-method | Show pairwisefst object |
| is.countdata | Check countdata objects |
| is.fitted.graph | Check fitted.graph objects |
| is.fstats | Check fstats objects |
| is.graph.params | Check graph.params objects |
| is.pairwisefst | Check pairwisefst objects |
| is.pooldata | Check pooldata objects |
| make.example.files | Create example files |
| pairwisefst-class | S4 class to represent a pairwise Fst results obtained with... |
| plot-fitted.graph-method | plot pairwisefst object |
| plot_fstats | Plot F2, F3, F3star, F4, D or pairwise Fst values with their... |
| plot-fstats-method | plot fstats object |
| plot-graph.params-method | plot graph in graph.params object |
| plot-pairwisefst-method | plot pairwisefst object |
| pooldata2diyabc | Convert a pooldata object into DIYABC input files. |
| pooldata2genobaypass | Convert a pooldata object into BayPass input files. |
| pooldata2genoselestim | Convert a pooldata object into SelEstim input files. |
| pooldata-class | S4 class to represent a Pool-Seq data set. |
| pooldata.subset | Create a subset of the pooldata object that contains Pool-Seq... |
| poolfstat | PoolFstat |
| poppair_idx | poppair_idx |
| popsync2pooldata | Convert Popoolation Sync files into a pooldata object |
| randomallele.pca | PCA of a pooldata or countdata object using a random allele... |
| rooted.njtree.builder | Construct and root an Neighbor-Joining tree of presumably... |
| scan_allele_info | scan_allele_info |
| show-countdata-method | Show countdata object |
| show-fitted.graph-method | Show fitted.graph object |
| show-fstats-method | Show fstats object |
| show-graph.params-method | Show graph.params object |
| show-pairwisefst-method | Show pairwisefst object |
| show-pooldata-method | Show pooldata object |
| sim.readcounts | Simulate read counts from count data and return a pooldata... |
| simureads_mono | simureads_mono |
| simureads_poly | simureads_poly |
| sliding.windows.fstat | Compute sliding window estimates of F-statistics or ratio of... |
| vcf2pooldata | Convert a VCF file into a pooldata object. |
