Man pages for rphast
Interface to 'PHAST' Software for Comparative Genomics
| add.introns.feat | Add introns to features |
| add.ls.mod | Add a lineage-specific model |
| add.signals.feat | Add start/stop codon, 3'/5' splice signals to features |
| add.UTRs.feat | Add UTRs to features |
| alphabet.msa | MSA Alphabet |
| apply.bgc.sel | Apply bgc+selection parameters to a matrix |
| as.data.frame.feat | Features to Data Frame |
| as.list.tm | Tree Model to List |
| as.pointer.feat | Features To Pointer |
| as.pointer.msa | MSA To Pointer |
| as.track.feat | Create a features track |
| as.track.msa | Create an alignment track |
| as.track.wig | Create a wig track |
| base.freq.msa | Get the frequencies of characters in an alignment |
| bgc.informative | Return features indicating regions informative for bgc |
| bgc.nucleotide.tests | Do maximum likelihood analysis for gBGC and selection using... |
| bgc.sel.factor | BGC+selection factor |
| branchlength.tree | Get the total length of the edges of a tree |
| classify.muts.bgc | Count the number of mutations of each gBGC type on each... |
| codon.clean.msa | Clean an alignment for codon analysis |
| col.expected.subs.msa | Obtain expected number of substitutions on each branch for... |
| complement | complement |
| composition.feat | Composition of features with respect to annotations |
| concat.msa | Concatenate msa objects |
| convert.coords.feat | Convert coordinates from one frame of reference to another |
| coord.range.msa | Obtain the range of coordinates in a MSA objects |
| copy.feat | Features copy |
| copy.msa | MSA copy |
| coverage.feat | Features coverage |
| density.feat | Features kernel density |
| depth.tree | Get the distance from a node to the root of a tree |
| dim.feat | Feature dimensions |
| dim.msa | Returns the dimensions of an msa object as (# of species, #... |
| enrichment.feat | Enrichment of features with respect to annotation types |
| expected.subs.msa | Obtain expected number of substitutions on each branch and... |
| extract.feature.msa | Extract features from an MSA object |
| feat | Features Objects |
| fix.semicolon.tree | Add a semi-colon to end of tree string |
| fix.start.stop.feat | Fix start and stop signals |
| flatten.feat | Combine adjacent features with the same "feature" field |
| freq3x4.msa | Get codon frequencies based on 3x4 model |
| from.pointer.feat | Convert a features object from C memory (external pointer) to... |
| from.pointer.msa | MSA From Pointer |
| gc.content.msa | Get the fraction of G's and C's in an alignment |
| get4d.msa | Extract fourfold degenerate sites from an MSA object |
| get.rate.matrix.params.tm | Get the parameters describing a rate matrix |
| guess.format.msa | MSA Guess Format |
| hist.feat | plot histogram of feature lengths |
| hmm | Create an rphast HMM object |
| informative.regions.msa | Get informative regions of an alignment |
| inverse.feat | Get inverse features |
| is.format.msa | Check an MSA Format String |
| is.msa | Check an MSA object |
| is.ordered.msa | MSA is Ordered? |
| is.subst.mod.tm | Check Substitution Model Strings |
| is.tm | Tree Models |
| is.track | Is this a track? |
| label.branches | Label tree branches |
| label.subtree | Label subtree |
| leafnames.tree | Get the names of a tree's leaf nodes |
| likelihood.msa | MSA Likelihood |
| mod.backgd.tm | Adjust tree model background frequencies while maintaining... |
| msa | MSA Objects |
| name.ancestors | Name Ancestral Nodes |
| names.msa | MSA Sequence Names |
| ncol.feat | Number of Columns in Features |
| ncol.msa | MSA Sequence Length. |
| ninf.msa | The number of informative columns in an alignment |
| nothanks.rphast | Stop rphast registration reminders |
| nrow.feat | Number of Features |
| nrow.msa | MSA Number of Sequences |
| nstate.hmm | HMM number of states |
| numleaf.tree | Number of leaves in a Tree |
| numnodes.tree | Number of Nodes in a Tree |
| offset.msa | MSA Index Offset |
| optim.rphast | Optimize using phast's optimization code |
| overlap.feat | Feature overlap |
| pairwise.diff.msa | Get pairwise differences per site between sequences |
| phastBias | phastBias |
| phastCons | Produce conservation scores and identify conserved elements,... |
| phyloFit | Fit a Phylogenetic model to an alignment... |
| phyloP | phyloP (basewise or by feature) |
| phyloP.prior | phyloP prior |
| phyloP.sph | phyloP SPH |
| plot.feat | Features plot |
| plot.gene | Gene plot |
| plot.lsmodel.tm | Make a bubble plot of a lineage-specific transition matrix of... |
| plot.msa | Plot an alignment |
| plot.rate.matrix | Make a bubble plot of a transition matrix |
| plot.tm | Make a bubble plot of the transition matrix for a tree model. |
| plot.track | Make browser-like plot in rphast |
| postprob.msa | Obtain posterior probilities of every state at every node |
| print.feat | Printing a features Object |
| print.msa | Printing MSA objects |
| print.phastBiasResult | Pretty-print the phastBias result list without spilling giant... |
| print.tm | Printing Tree Models |
| prune.tree | Prune a Tree |
| range.feat | Features range |
| range.track | Get the coordinate range of a list of RPHAST results |
| rbind.feat | concatenate feature objects |
| read.feat | Read a Feature File (GFF, BED, or GenePred) |
| read.hmm | Read an HMM object from a file |
| read.msa | Reading an MSA Object |
| read.newick.tree | Read a Newick Tree from a File |
| read.tm | Read a Tree Model |
| read.wig | Read a wig file |
| reflect.phylo.hmm | Reflect a phylo-hmm across a strand |
| register.rphast | Register RPHAST |
| rename.tree | Tree Node Renaming |
| rescale.tree | Scale a Tree or Subtree |
| reverse.complement.msa | Reverse complement a multiple sequence alignment |
| rphast-package | Interface to 'PHAST' Software for Comparative Genomics |
| sample.msa | Sample columns from an MSA |
| score.hmm | Score an alignment using a general phylo-HMM |
| set.rate.matrix.tm | Set the rate matrix of a tree model using model-specific... |
| setup.branch.site.tm | Set up a tree model for branch site selection analysis |
| simulate.msa | Simulate a MSA given a tree model and HMM. |
| smooth.wig | Smooth a wig plot in rphast |
| sort.feat | Sort a GFF |
| split.by.feature.msa | Split an MSA by feature |
| split.feat | Split features by length |
| square-bracket-assign-msa | Replace subsets of an alignment |
| square-bracket-msa | Extract, replace, reorder MSA |
| state.freq.msa | Get the observed frequencies of states in an alignment |
| strip.gaps.msa | MSA Strip Gaps |
| sub.msa | MSA Subset |
| subst.mods | List PHAST Substitution Models |
| subtree | Subtree |
| summary.feat | Features Summary |
| summary.msa | MSA Summary |
| summary.tm | Tree Model Summary |
| summary.tree | Get a summary of a Newick-formatted tree, edge lengths, node... |
| tagval | Extract value from tag-value formatted attributes |
| tagval.feat | Extract value from tag-value formatted attribute in features... |
| tm | Tree Models |
| total.expected.subs.msa | Obtain expected number of substitutions of each type on each... |
| translate.msa | Get amino acid sequences from an alignment |
| unapply.bgc.sel | Unapply bgc+selection parameters from a matrix |
| unique.feat | Remove overlapping genes |
| write.feat | Writing a features Object |
| write.hmm | Write an HMM object to a file |
| write.msa | Writing MSA Objects to Files |
| write.tm | Wrting Tree Models |
| write.wig | Writing a wig file |
| write.wig.feat | Write a features object in fixedStep wig format |
