RPHAST: R interface to PHAST


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Documentation for package ‘rphast’ version 1.1

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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...