Provides an R interface to the 'PHAST'(<http://compgen.cshl.edu/phast/>) software (Phylogenetic Analysis with Space/Time Models). It can be used for many types of analysis in comparative and evolutionary genomics, such as estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and predicting elements based on conservation or custom phylogenetic hidden Markov models. It can also perform many basic operations on multiple sequence alignments and phylogenetic trees.
| Copyright: | All code is Copyright (c) 2002-2018 University |
| of California, Cornell University, Cold Spring Harbor Laboratory. | |
| Package: | rphast |
| License: | BSD_3_clause + file LICENSE |
| Version: | 1.6.9 |
| URL: | http://compgen.cshl.edu/rphast |
| Date: | 2018-01-30 |
| Imports: | methods |
| Depends: | |
| stats | |
| Suggests: | |
| ape, | |
| seqLogo | |
| Collate: | |
| 'bgc.R' | |
| 'checkArgs.R' | |
| 'feat.R' | |
| 'hmm.R' | |
| 'listOfLists.R' | |
| 'msa.R' | |
| 'optim.R' | |
| 'phastCons.R' | |
| 'phyloFit.R' | |
| 'phyloP.R' | |
| 'plot.R' | |
| 'rphast.R' | |
| 'treeModel.R' | |
| 'trees.R' | |
| 'zzz.R' | |
| RoxygenNote: | 5.0.1 |
| Built: | R 3.1.2; x86_64-unknown-linux-gnu; 2018-01-30 15:53:11 UTC; unix |
Index:
[.msa Extract, replace, reorder MSA
[<-.msa Replace subsets of an alignment
add.UTRs.feat Add UTRs to features
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
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 nucleotide model
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 branch
codon.clean.msa Clean an alignment for codon analysis
col.expected.subs.msa Obtain expected number of substitutions on each
branch for each site pattern and each
substitution type
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, # of columns)
enrichment.feat Enrichment of features with respect to
annotation types
expected.subs.msa Obtain expected number of substitutions on each
branch and site
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 R memory
from.pointer.msa MSA From Pointer
gc.content.msa Get the fraction of G's and C's in an alignment
get.rate.matrix.params.tm
Get the parameters describing a rate matrix
get4d.msa Extract fourfold degenerate sites from an MSA
object
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 reversibility
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, given a multiple alignment
and a phylo-HMM.
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 a tree model.
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 matrices onto the screen
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
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 parameters.
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
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 names, etc
tagval Extract value from tag-value formatted
attributes
tagval.feat Extract value from tag-value formatted
attribute in features object
tm Tree Models
total.expected.subs.msa
Obtain expected number of substitutions of each
type on each branch
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