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rphast (version 1.0)

RPHAST

Description

R interface to PHAST

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Version

Install

install.packages('rphast')

Monthly Downloads

10

Version

1.0

License

GPL (>= 2)

Maintainer

Melissa Hubisz

Last Published

September 15th, 2010

Functions in rphast (1.0)

as.pointer.feat

Features To Pointer
plot.track

Make browser-like plot in rphast...
as.pointer.msa

MSA To Pointer
depth.tree

Get the distance from a node to the root of a tree...
as.list.tm

Tree Model to List
msa

MSA Objects
[.msa

Extract, replace, reorder MSA...
guess.format.msa

MSA Format From Filename Extension
addSignals.feat

Add start/stop codon, 3'/5' splice signals to features...
print.msa

Printing MSA objects
ncol.msa

MSA Sequence Length.
feat.track

Create a features track...
concat.msa

Concatenate msa objects...
read.tm

Read a Tree Model
density.feat

Features kernel density...
smooth.wig

Smooth a wig plot in rphast...
branchlen.tree

Get the total length of the edges of a tree...
complement

complement
is.tm

Tree Models
nrow.msa

MSA Number of Sequences
composition.feat

Composition of features with respect to annotations...
rename.tree

Tree Node Renaming
range.feat

Features range
sort.feat

Sort a GFF...
rphast-package

RPHAST
copy.msa

MSA copy
dim.feat

Feature dimensions
extract.feature.msa

Extract features from an MSA object...
gene.track

Create a gene track...
range.track

Get the coordinate range of a list of RPHAST results...
copy.feat

Features copy
summary.tm

Tree Model Summary
coverage.feat

Features coverage...
nrow.feat

Number of Features
name.ancestors

Name Ancestral Nodes
addIntrons.feat

Add introns to features...
alphabet.msa

MSA Alphabet
enrichment.feat

Enrichment of features with respect to annotation types...
print.feat

Printing a features Object
write.feat

Writing a features Object
likelihood.msa

MSA Likelihood
get4d.msa

Extract fourfold degenerate sites from an MSA object...
wig.track

Create a wig track...
dim.msa

Returns the dimensions of an msa object as (# of species, # of columns)...
rbind.feat

concatenate feature objects...
phyloP.prior

phyloP prior
strip.gaps.msa

MSA Strip Gaps
is.ordered.msa

MSA is Ordered?
write.hmm

Write an HMM object to a file...
informative.regions.msa

Get informative regions of an alignment...
as.data.frame.feat

Features to Data Frame
fix.semicolon.tree

Add a semi-colon to end of tree string...
offset.msa

MSA Index Offset
hist.feat

plot histogram of feature lengths...
isSubstMod.tm

Check Substitution Model Strings
overlap.feat

Feature overlap...
from.pointer.msa

MSA From Pointer
ncol.feat

Number of Columns in Features
read.hmm

Read an HMM object from a file...
phyloP.sph

phyloP SPH
reverse.complement

Reverse complement a multiple sequence alignment...
unique.feat

Remove overlapping genes...
feat

Features Objects
inverse.feat

Get inverse features...
split.by.feature.msa

Split an MSA by feature...
ninf.msa

The number of informative columns in an alignment...
summary.msa

MSA Summary
tagval

Extract value from tag-value formatted attributes...
fixStartStop.feat

Fix start and stop signals...
print.tm

Printing Tree Models
names.msa

MSA Sequence Names
nstate.hmm

HMM number of states...
is.msa

Check an MSA object...
plot.gene

Gene plot
read.feat

Read a Feature File (GFF, BED, or GenePred)
write.tm

Wrting Tree Models
rescale.tree

Scale a Tree or Subtree
phyloP

phyloP (basewise or by feature)
plot.feat

Features plot
hmm

Create an rphast HMM object
validFormatStr.msa

Check an MSA Format String
prune.tree

Prune a Tree
sub.msa

MSA Subset
is.track

Is this a track?
subtree

Subtree
simulate.msa

Simulate a MSA given a tree model and HMM.
score.hmm

Score an alignment using a general phylo-HMM
tagval.feat

Extract value from tag-value formatted attribute in features object...
addUTRs.feat

Add UTRs to features...
write.msa

Writing MSA Objects to Files
sample.msa

Sample columns from an MSA...
phastCons

Produce conservation scores and identify conserved elements,...
read.newick.tree

Read a Newick Tree from a File
split.feat

Split features by length...
summary.feat

Features Summary
subst.mods

List PHAST Substitution Models
read.msa

Reading an MSA Object
phyloFit

Fit a Phylogenetic model to an alignment...
numnodes.tree

Number of Nodes in a Tree
tm

Tree Models