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version 1.4
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mjhubisz authored and gaborcsardi committed Feb 8, 2011
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34 changes: 34 additions & 0 deletions ChangeLog
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3-26-2013: 1.4
* added gBGC functions phastBias, bgc.nucleotide.tests, and
classify.muts.bgc
* changed all "alt.mod" to "ls.mod" (lineage-specific)
* added nuc.text (and options nuc.text.pos, nuc.text.col) options to
plot.msa and as.track.msa; this is for plotting additional text
along the top or bottom of an alignment.
* fixed bug in alt.mod.tm (was ignoriong rate.matrix argument, which
has been removed)
* modified overlap.feat to return list of two gffs when
get.fragments==TRUE (one containing fragments and another containing
features that selected the fragments)
* modified sort.feat to sort first by seqname, then by position
* added flatten.feat which merges adjacent features of the same type
* fixed bug in as.track.msa which (refseq arg was ignored)
* changed definition of selection in lineage-specific models to be
the sum of mod$selection + mod$altmod$selection
* fixed bug causing segfault in concat.msa
* added max.EM.its argument to phyloFit
* added optim.rphast function
* updates to feat object; now it belongs to classes "feat" and
"data.frame"
* update to guess.format.msa; now it opens up files and guesses format
based on contents by default.
* added freq3x4.msa to calculate codon frequencies of an alignment using
3x4 model
* added site.model flag to tree model object which indicates whether
a tree model represents a Nielsen-Yang site model
* added function setup.branch.site.tm which takes a tree model and
returns a tree model representing a branch-site model with a
specified foreground branch. The site-model can optionally
include extra site categories with bgc on the foreground branch.
* changed tagval and tagval.feat to work with either GFF 2 or 3
specification
12-22-2010 : 1.3
* improvements to memory handler, which previously slowed down rphast
by 33%. Now there is no significant increase in run-time, at least
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25 changes: 13 additions & 12 deletions DESCRIPTION
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Copyright: The code in src/pcre is Copyright (c) 1997-2010 University
of Cambridge. All other code is Copyright (c) 2002-2010
University of California, Cornell University.
Package: rphast
Version: 1.3
Date: 2010-11-01
Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>
License: BSD
Title: R interface to PHAST software for comparative genomics
Author: Melissa Hubisz, Katherine Pollard, and Adam Siepel
Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>
Description: RPHAST is an R interface to the PHAST pacakge
(Phylogenetic Analyis with Space/Time Models). It can be used
for many types of analysis in comparative and evolutionary
Expand All @@ -13,16 +15,15 @@ Description: RPHAST is an R interface to the PHAST pacakge
phylogenetic hidden Markov models. It can also perform many
basic operations on multiple sequence alignments and
phylogenetic trees.
License: BSD
Version: 1.4
URL: http://compgen.bscb.cornell.edu/rphast
Copyright: The code in src/pcre is Copyright (c) 1997-2010 University
of Cambridge. All other code is Copyright (c) 2002-2010
University of California, Cornell University.
Date: 2011-02-08
Depends: stats
Suggests: ape, seqLogo
Collate: 'checkArgs.R' 'feat.R' 'hmm.R' 'listOfLists.R' 'msa.R'
'phastCons.R' 'phyloFit.R' 'phyloP.R' 'plot.R' 'rphast.R'
'treeModel.R' 'trees.R'
Packaged: 2010-12-22 17:02:24 UTC; melissa
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'
Packaged: 2013-03-28 17:21:08 UTC; melissa
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2010-12-23 10:28:59
Date/Publication: 2013-03-28 19:53:07
655 changes: 384 additions & 271 deletions MD5
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287 changes: 158 additions & 129 deletions NAMESPACE
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export(copy.feat)
export(read.feat)
export(feat)
export(as.pointer.feat)
export(print.feat)
S3method(print, feat)
export(write.feat)
export(nrow.feat)
S3method(nrow, feat)
export(ncol.feat)
S3method(ncol, feat)
export(summary.feat)
S3method(summary, feat)
export(as.data.frame.feat)
S3method(as.data.frame, feat)
export(dim.feat)
S3method(dim, feat)
S3method(range, feat)
export(range.feat)
S3method(plot, feat)
export(plot.feat)
export(plot.gene)
export(density.feat)
S3method(hist, feat)
export(hist.feat)
export(overlap.feat)
export(inverse.feat)
export(coverage.feat)
export(add.UTRs.feat)
export(add.introns.feat)
export(add.ls.mod)
export(add.signals.feat)
export(fix.start.stop.feat)
export(rbind.feat)
export(split.feat)
export(sort.feat)
S3method(sort, feat)
export(add.UTRs.feat)
export(alphabet.msa)
export(apply.bgc.sel)
export(as.data.frame.feat)
export(as.list.tm)
export(as.pointer.feat)
export(as.pointer.msa)
export(as.track.feat)
export(as.track.msa)
export(as.track.wig)
export(base.freq.msa)
export(bgc.informative)
export(bgc.nucleotide.tests)
export(bgc.sel.factor)
export(branchlength.tree)
export(classify.muts.bgc)
export(codon.clean.msa)
export(col.expected.subs.msa)
export(complement)
export(composition.feat)
export(concat.msa)
export(coord.range.msa)
export(copy.feat)
export(copy.msa)
export(coverage.feat)
export(density.feat)
export(depth.tree)
export(dim.feat)
export(dim.msa)
export(enrichment.feat)
S3method(unique, feat)
export(unique.feat)
export(tagval.feat)
export(tagval)
export(expected.subs.msa)
export(extract.feature.msa)
export(feat)
export(fix.semicolon.tree)
export(fix.start.stop.feat)
export(flatten.feat)
export(freq3x4.msa)
export(from.pointer.feat)
export(from.pointer.msa)
export(gc.content.msa)
export(get4d.msa)
export(get.rate.matrix.params.tm)
export(guess.format.msa)
export(hist.feat)
export(hmm)
export(read.hmm)
export(write.hmm)
export(nstate.hmm)
export(score.hmm)
export(copy.msa)
export(informative.regions.msa)
export(inverse.feat)
export(is.format.msa)
export(is.msa)
useDynLib(rphast)
export(is.ordered.msa)
export(is.subst.mod.tm)
export(is.tm)
export(is.track)
export(label.branches)
export(label.subtree)
export(leafnames.tree)
export(likelihood.msa)
export(mod.backgd.tm)
export("[<-.msa")
export("[.msa")
export(msa)
export(name.ancestors)
export(names.msa)
export(ncol.feat)
export(ncol.msa)
S3method(ncol, msa)
export(coord.range.msa)
S3method(dim, msa)
export(dim.msa)
export(ninf.msa)
export(nothanks.rphast)
export(nrow.feat)
export(nrow.msa)
S3method(nrow, msa)
export(is.format.msa)
export(nstate.hmm)
export(numleaf.tree)
export(numnodes.tree)
export(offset.msa)
export(alphabet.msa)
export(is.ordered.msa)
S3method(is.ordered, msa)
export(names.msa)
S3method(names, msa)
export(from.pointer.msa)
export(as.pointer.msa)
export(guess.format.msa)
export(write.msa)
export(summary.msa)
S3method(summary, msa)
export(print.msa)
S3method(print, msa)
export(read.msa)
export(complement)
export(reverse.complement.msa)
export(sub.msa)
export(strip.gaps.msa)
S3method("[", msa)
export("[.msa")
export(postprob.msa)
export(expected.subs.msa)
export(total.expected.subs.msa)
export(col.expected.subs.msa)
export(likelihood.msa)
export(simulate.msa)
importFrom(stats, simulate)
S3method(simulate, msa)
S3method(sample, msa)
export(sample.msa)
export(get4d.msa)
export(extract.feature.msa)
export(concat.msa)
export(split.by.feature.msa)
export(informative.regions.msa)
export(codon.clean.msa)
export(state.freq.msa)
export(base.freq.msa)
export(gc.content.msa)
export(optim.rphast)
export(overlap.feat)
export(pairwise.diff.msa)
export(translate.msa)
export(plot.msa)
export(phastBias)
export(phastCons)
export(phyloFit)
export(phyloP)
export(phyloP.prior)
export(phyloP.sph)
export(is.track)
export(range.track)
export(smooth.wig)
export(plot.track)
export(as.track.wig)
export(as.track.msa)
export(as.track.feat)
export(is.tm)
export(read.tm)
export(write.tm)
export(summary.tm)
S3method(summary, tm)
export(as.list.tm)
S3method(as.list, tm)
export(print.tm)
S3method(print, tm)
export(is.subst.mod.tm)
export(subst.mods)
export(tm)
export(mod.backgd.tm)
export(bgc.sel.factor)
export(apply.bgc.sel)
export(unapply.bgc.sel)
export(add.alt.mod)
export(set.rate.matrix.tm)
export(get.rate.matrix.params.tm)
export(plot.feat)
export(plot.gene)
export(plot.lsmodel.tm)
export(plot.msa)
export(plot.rate.matrix)
export(plot.tm)
export(plot.altmodel.tm)
export(fix.semicolon.tree)
export(read.newick.tree)
export(numnodes.tree)
export(numleaf.tree)
export(branchlength.tree)
export(depth.tree)
export(plot.track)
export(postprob.msa)
export(print.feat)
export(print.msa)
export(print.tm)
export(prune.tree)
export(name.ancestors)
export(subtree)
export(rescale.tree)
export(range.feat)
export(range.track)
export(rbind.feat)
export(read.feat)
export(read.hmm)
export(read.msa)
export(read.newick.tree)
export(read.tm)
export(read.wig)
export(register.rphast)
export(rename.tree)
export(label.branches)
export(label.subtree)
export(rescale.tree)
export(reverse.complement.msa)
export(sample.msa)
export(score.hmm)
export(set.rate.matrix.tm)
export(setup.branch.site.tm)
export(simulate.msa)
export(smooth.wig)
export(sort.feat)
export(split.by.feature.msa)
export(split.feat)
export(state.freq.msa)
export(strip.gaps.msa)
export(sub.msa)
export(subst.mods)
export(subtree)
export(summary.feat)
export(summary.msa)
export(summary.tm)
export(summary.tree)
export(tagval)
export(tagval.feat)
export(tm)
export(total.expected.subs.msa)
export(translate.msa)
export(unapply.bgc.sel)
export(unique.feat)
export(write.feat)
export(write.hmm)
export(write.msa)
export(write.tm)
export(write.wig)
export(write.wig.feat)
importFrom(stats,density)
importFrom(stats,simulate)
S3method(as.data.frame,feat)
S3method(as.list,tm)
S3method(density,feat)
S3method(dim,feat)
S3method(dim,msa)
S3method(hist,feat)
S3method(is.ordered,msa)
S3method("[",msa)
S3method(names,msa)
S3method(ncol,feat)
S3method(ncol,msa)
S3method(nrow,feat)
S3method(nrow,msa)
S3method(plot,feat)
S3method(plot,gene)
S3method(plot,lsmodel.tm)
S3method(plot,msa)
S3method(plot,rate.matrix)
S3method(plot,tm)
S3method(plot,track)
S3method(print,feat)
S3method(print,msa)
S3method(print,phastBiasResult)
S3method(print,tm)
S3method(range,feat)
S3method(range,track)
S3method(sample,msa)
S3method(simulate,msa)
S3method(sort,feat)
S3method(split,by.feature.msa)
S3method(split,feat)
S3method(summary,feat)
S3method(summary,msa)
S3method(summary,tm)
S3method(summary,tree)
S3method(unique,feat)
useDynLib(rphast)

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