Index: [.msa Extract, replace, reorder MSA... 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 branchlen.tree Get the total length of the edges of a tree... 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... 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)... enrichment.feat Enrichment of features with respect to annotation types... extract.feature.msa Extract features from an MSA object... 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 gene.track Create a gene track... get4d.msa Extract fourfold degenerate sites from an MSA object... guess.format.msa MSA Format From Filename Extension hist.feat plot histogram of feature lengths... hmm Create an rphast HMM object 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 likelihood.msa MSA Likelihood msa MSA Objects 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 offset.msa MSA Index Offset overlap.feat Feature overlap... 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 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... 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 tagval Extract value from tag-value formatted attributes... tagval.feat Extract value from tag-value formatted attribute in features object... tm Tree Models unique.feat Remove overlapping genes... validFormatStr.msa Check an MSA Format String 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
Further information is available in the following vignettes:
vignette1 rphast (source, pdf)
vignette2 rphast (source, pdf)
vignette3 rphast (source, pdf)
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