- rphast: Interface to PHAST Software for Comparative Genomics
- print.feat: Printing a features Object
Printing a features Object
Prints a features object.
an object of type
further arguments to be passed to or from other methods
Melissa J. Hubisz and Adam Siepel
Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.
- 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