R interface to PHAST software for comparative genomics


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Documentation for package ‘rphast’ version 1.3

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A B C D E F G H I L M N O P R S T U W misc

-- --

rphast-package R interface to PHAST software for comparative genomics

-- A --

add.alt.mod Add a lineage-specific model...
add.introns.feat Add introns to features...
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...

-- B --

base.freq.msa Get the frequencies of characters in an alignment...
bgc.sel.factor BGC+selection factor...
branchlength.tree Get the total length of the edges of a tree...

-- C --

codon.clean.msa Clean an alignment for codon analysis...
col.expected.subs.msa Obtain expected number of substitutions on each branch for each site...
complement complement
composition.feat Composition of features with respect to annotations...
concat.msa Concatenate msa objects...
coord.range.msa Obtain the range of coordinates in a MSA objects...
copy.feat Features copy
copy.msa MSA copy
coverage.feat Features coverage...

-- D --

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)...

-- E --

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...

-- F --

feat Features Objects
fix.semicolon.tree Add a semi-colon to end of tree string...
fix.start.stop.feat Fix start and stop signals...
from.pointer.msa MSA From Pointer

-- G --

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 Format From Filename Extension

-- H --

hist.feat plot histogram of feature lengths...
hmm Create an rphast HMM object

-- I --

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?

-- L --

label.branches Label tree branches
label.subtree Label subtree
likelihood.msa MSA Likelihood

-- M --

mod.backgd.tm Adjust tree model background frequencies while maintaining reversibility...
msa MSA Objects

-- N --

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...
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

-- O --

offset.msa MSA Index Offset
overlap.feat Feature overlap...

-- P --

pairwise.diff.msa Get pairwise differences per site between sequences...
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.altmodel.tm Make a bubble plot of a lineage-specific transition matrix of a...
plot.feat Features plot
plot.gene Gene plot
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.tm Printing Tree Models
prune.tree Prune a Tree

-- R --

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
rename.tree Tree Node Renaming
rescale.tree Scale a Tree or Subtree
reverse.complement.msa Reverse complement a multiple sequence alignment...
rphast R interface to PHAST software for comparative genomics

-- S --

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.
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...

-- T --

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 on each branch...
translate.msa Get amino acid sequences from an alignment...

-- U --

unapply.bgc.sel Unapply bgc+selection parameters from a matrix...
unique.feat Remove overlapping genes...

-- W --

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

-- misc --

[.msa Extract, replace, reorder MSA...