Man pages for rphast
Interface to 'PHAST' Software for Comparative Genomics

add.introns.featAdd introns to features a lineage-specific model
add.signals.featAdd start/stop codon, 3'/5' splice signals to features
add.UTRs.featAdd UTRs to features
alphabet.msaMSA Alphabet
apply.bgc.selApply bgc+selection parameters to a matrix to Data Frame
as.list.tmTree Model to List
as.pointer.featFeatures To Pointer
as.pointer.msaMSA To Pointer
as.track.featCreate a features track
as.track.msaCreate an alignment track
as.track.wigCreate a wig track
base.freq.msaGet the frequencies of characters in an alignment
bgc.informativeReturn features indicating regions informative for bgc
bgc.nucleotide.testsDo maximum likelihood analysis for gBGC and selection using...
bgc.sel.factorBGC+selection factor
branchlength.treeGet the total length of the edges of a tree
classify.muts.bgcCount the number of mutations of each gBGC type on each...
codon.clean.msaClean an alignment for codon analysis
col.expected.subs.msaObtain expected number of substitutions on each branch for...
composition.featComposition of features with respect to annotations
concat.msaConcatenate msa objects
convert.coords.featConvert coordinates from one frame of reference to another
coord.range.msaObtain the range of coordinates in a MSA objects
copy.featFeatures copy
copy.msaMSA copy
coverage.featFeatures coverage
density.featFeatures kernel density
depth.treeGet the distance from a node to the root of a tree
dim.featFeature dimensions
dim.msaReturns the dimensions of an msa object as (# of species, #...
enrichment.featEnrichment of features with respect to annotation types
expected.subs.msaObtain expected number of substitutions on each branch and...
extract.feature.msaExtract features from an MSA object
featFeatures Objects
fix.semicolon.treeAdd a semi-colon to end of tree string
fix.start.stop.featFix start and stop signals
flatten.featCombine adjacent features with the same "feature" field
freq3x4.msaGet codon frequencies based on 3x4 model
from.pointer.featConvert a features object from C memory (external pointer) to...
from.pointer.msaMSA From Pointer
gc.content.msaGet the fraction of G's and C's in an alignment
get4d.msaExtract fourfold degenerate sites from an MSA object
get.rate.matrix.params.tmGet the parameters describing a rate matrix
guess.format.msaMSA Guess Format
hist.featplot histogram of feature lengths
hmmCreate an rphast HMM object
informative.regions.msaGet informative regions of an alignment
inverse.featGet inverse features
is.format.msaCheck an MSA Format String
is.msaCheck an MSA object
is.ordered.msaMSA is Ordered?
is.subst.mod.tmCheck Substitution Model Strings
is.tmTree Models
is.trackIs this a track?
label.branchesLabel tree branches
label.subtreeLabel subtree
leafnames.treeGet the names of a tree's leaf nodes
likelihood.msaMSA Likelihood
mod.backgd.tmAdjust tree model background frequencies while maintaining...
msaMSA Objects
name.ancestorsName Ancestral Nodes
names.msaMSA Sequence Names
ncol.featNumber of Columns in Features
ncol.msaMSA Sequence Length.
ninf.msaThe number of informative columns in an alignment
nothanks.rphastStop rphast registration reminders
nrow.featNumber of Features
nrow.msaMSA Number of Sequences
nstate.hmmHMM number of states
numleaf.treeNumber of leaves in a Tree
numnodes.treeNumber of Nodes in a Tree
offset.msaMSA Index Offset
optim.rphastOptimize using phast's optimization code
overlap.featFeature overlap
pairwise.diff.msaGet pairwise differences per site between sequences
phastConsProduce conservation scores and identify conserved elements,...
phyloFitFit a Phylogenetic model to an alignment...
phyloPphyloP (basewise or by feature)
phyloP.priorphyloP prior
phyloP.sphphyloP SPH
plot.featFeatures plot
plot.geneGene plot
plot.lsmodel.tmMake a bubble plot of a lineage-specific transition matrix of...
plot.msaPlot an alignment
plot.rate.matrixMake a bubble plot of a transition matrix
plot.tmMake a bubble plot of the transition matrix for a tree model.
plot.trackMake browser-like plot in rphast
postprob.msaObtain posterior probilities of every state at every node
print.featPrinting a features Object
print.msaPrinting MSA objects
print.phastBiasResultPretty-print the phastBias result list without spilling giant...
print.tmPrinting Tree Models
prune.treePrune a Tree
range.featFeatures range
range.trackGet the coordinate range of a list of RPHAST results
rbind.featconcatenate feature objects
read.featRead a Feature File (GFF, BED, or GenePred)
read.hmmRead an HMM object from a file
read.msaReading an MSA Object
read.newick.treeRead a Newick Tree from a File
read.tmRead a Tree Model
read.wigRead a wig file
reflect.phylo.hmmReflect a phylo-hmm across a strand
register.rphastRegister RPHAST
rename.treeTree Node Renaming
rescale.treeScale a Tree or Subtree
reverse.complement.msaReverse complement a multiple sequence alignment
rphast-packageInterface to 'PHAST' Software for Comparative Genomics
sample.msaSample columns from an MSA
score.hmmScore an alignment using a general phylo-HMM
set.rate.matrix.tmSet the rate matrix of a tree model using model-specific... up a tree model for branch site selection analysis
simulate.msaSimulate a MSA given a tree model and HMM.
smooth.wigSmooth a wig plot in rphast
sort.featSort a GFF an MSA by feature
split.featSplit features by length
square-bracket-assign-msaReplace subsets of an alignment
square-bracket-msaExtract, replace, reorder MSA
state.freq.msaGet the observed frequencies of states in an alignment
strip.gaps.msaMSA Strip Gaps
sub.msaMSA Subset
subst.modsList PHAST Substitution Models
summary.featFeatures Summary
summary.msaMSA Summary
summary.tmTree Model Summary
summary.treeGet a summary of a Newick-formatted tree, edge lengths, node...
tagvalExtract value from tag-value formatted attributes
tagval.featExtract value from tag-value formatted attribute in features...
tmTree Models
total.expected.subs.msaObtain expected number of substitutions of each type on each...
translate.msaGet amino acid sequences from an alignment
unapply.bgc.selUnapply bgc+selection parameters from a matrix
unique.featRemove overlapping genes
write.featWriting a features Object
write.hmmWrite an HMM object to a file
write.msaWriting MSA Objects to Files
write.tmWrting Tree Models
write.wigWriting a wig file
write.wig.featWrite a features object in fixedStep wig format
rphast documentation built on Feb. 11, 2018, 5 p.m.