- rphast: Interface to PHAST Software for Comparative Genomics
- write.wig: Writing a wig file
Writing a wig file
Write a fixedStep wig file
A character vector giving chromosome name for each point. Will be recycled to length(start)
An integer vector giving start coordinate for each point.
A numeric vector giving score at each point Will be recycled to length(start)
An integer giving span (ie, length) of each element (all elements must have the same length, so only a single value is allowed).
The name of the file to write to (will be overwritten). A value of NULL implies write to console.
Whether to append to the file. If FALSE, file will be overwritten.
Melissa J. Hubisz
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- 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