R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Classification

Results 1 - 10 of 30 found.
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megaptera-internal (Package: megaptera) : Internal MEGAPTERA Functions

Internal megaptera functions.

● Data Source: CranContrib
● Keywords: internal
● Alias: EFetchHigherTaxon, EFetchLocus, MAD, NCBI.wrap, addNbAcc, alignGenus, calcDistToRef, check.TaxAgainstPhy, compare.phylo.backbone, conn, coverage, dbAutoFillTaxonomy, dbDeleteSpec, dbReadDNAbin, dbReadReference, dbUpdateLocus, dbWriteDNAbin, dbWriteString, dbconnect, downloadSequences, esearch, extractLocus, filter.alignment, fixTaxonomy, force.mp, funX, getGeneRange, getLineage, getMaxDist, insert.tip.phylo, is.alignable, loci, mafft.merge, markersGenbank, maxDist, maxDistMPI, meanPairwiseIdentity, megapteraHeatmap, myDist, ncbiLineage, nucleotideOverlap, pars, read.benchmark.db, revCompTest, select.seqs, slog, sortRanks, specCons, speciesConsensus, splitGiTaxon, sql.conform, sql.wrap, sqlTaxonomyHeader, stepAA, summary.sproj, supermatrix, tab, tax, tax2tree, term, unalignable, whereToInsert, write.dna.spectable
● 0 images

dbPars (Package: megaptera) : Set Database Parameters

Sets

● Data Source: CranContrib
● Keywords:
● Alias: dbPars
● 0 images

stepE (Package: megaptera) :

In stepE the genetic distance of each sequence from the corresponding benchmark sequence will be calculated and written to the postgreSQL database.

● Data Source: CranContrib
● Keywords:
● Alias: stepE
● 0 images

addTip (Package: megaptera) : Add Tips to a Phylogeny

This function adds tips (terminal nodes) to a (currently ultrametric) phylogenetic tree.

● Data Source: CranContrib
● Keywords:
● Alias: addTip
● 0 images

check.Functions (Package: megaptera) : Check SUSILI Results

This set of functions helps to check progress and consistency of a megaptera project.

● Data Source: CranContrib
● Keywords:
● Alias: check.Clades, check.Coverage, check.Markers, check.NameChanges, check.Species
● 0 images

strip.infraspec (Package: megaptera) :

Delete infraspecific names and epithets form species names.

● Data Source: CranContrib
● Keywords:
● Alias: strip.infraspec, strip.spec
● 0 images

prune.phylo.rank (Package: megaptera) : Prune Phylogenies

Prune tips of a certain taxonomic rank from an object of class phylo and obtain a new phylo object whose tips are of a higher rank.

● Data Source: CranContrib
● Keywords:
● Alias: prune.phylo.rank
● 0 images

megapteraPars (Package: megaptera) : Set Pipeline Parameters

Sets size limits, threshold values and other parameters that control the flow along the pipeline.

● Data Source: CranContrib
● Keywords:
● Alias: megapteraPars
● 0 images

locus-class (Package: megaptera) : Class "locus"

Class for genetic input parameters for megapteraProj.

● Data Source: CranContrib
● Keywords:
● Alias: locus-class
● 0 images

io.dna.db (Package: megaptera) :

DNA sequence alignment can be read from and written to a (alreay existing) pgSQL database table.

● Data Source: CranContrib
● Keywords:
● Alias: dbReadDNA, dbWriteDNA
● 0 images