# RPHAST: R interface to PHAST

## Documentation for package ‘rphast’ version 1.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- --

rphast-package | RPHAST: R interface to PHAST

## -- A --

addIntrons.feat | Add introns to features...
addSignals.feat | Add start/stop codon, 3'/5' splice signals to features...
addUTRs.feat | Add UTRs to features...
alphabet.msa | MSA Alphabet
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

## -- B --

branchlen.tree | Get the total length of the edges of a tree...

## -- C --

complement | complement
composition.feat | Composition of features with respect to annotations...
concat.msa | Concatenate 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...
extract.feature.msa | Extract features from an MSA object...

## -- F --

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

## -- G --

gene.track | Create a gene track...
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.msa | Check an MSA object...
is.ordered.msa | MSA is Ordered?
is.tm | Tree Models
is.track | Is this a track?
isSubstMod.tm | Check Substitution Model Strings

## -- L --

likelihood.msa | MSA Likelihood

## -- M --

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...
numnodes.tree | Number of Nodes in a Tree

## -- O --

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

## -- P --

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.track | Make browser-like plot in rphast...
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 | Reverse complement a multiple sequence alignment...
rphast | RPHAST: R interface to PHAST

## -- S --

sample.msa | Sample columns from an MSA...
score.hmm | Score an alignment using a general phylo-HMM
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...
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

## -- T --

tagval | Extract value from tag-value formatted attributes...
tagval.feat | Extract value from tag-value formatted attribute in features object...
tm | Tree Models

## -- U --

unique.feat | Remove overlapping genes...

## -- V --

validFormatStr.msa | Check an MSA Format String

## -- W --

wig.track | Create a wig track...
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...