Package: haplotypes 1.1.3.1
haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapses identical DNA sequences into haplotypes or inferring haplotypes using user provided absolute pairwise character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.
Authors:
haplotypes_1.1.3.1.tar.gz
haplotypes_1.1.3.1.zip(r-4.5)haplotypes_1.1.3.1.zip(r-4.4)haplotypes_1.1.3.1.zip(r-4.3)
haplotypes_1.1.3.1.tgz(r-4.4-any)haplotypes_1.1.3.1.tgz(r-4.3-any)
haplotypes_1.1.3.1.tar.gz(r-4.5-noble)haplotypes_1.1.3.1.tar.gz(r-4.4-noble)
haplotypes_1.1.3.1.tgz(r-4.4-emscripten)haplotypes_1.1.3.1.tgz(r-4.3-emscripten)
haplotypes.pdf |haplotypes.html✨
haplotypes/json (API)
| # Install 'haplotypes' in R: |
| install.packages('haplotypes', repos = c('https://cnrakt.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cnrakt/haplotypes/issues
- dna.obj - Example DNA sequence data
Last updated 1 years agofrom:b4bf6e0818. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 17 2024 |
| R-4.5-win | NOTE | Sep 17 2024 |
| R-4.5-linux | NOTE | Sep 17 2024 |
| R-4.4-win | OK | Sep 17 2024 |
| R-4.4-mac | OK | Sep 17 2024 |
| R-4.3-win | OK | Sep 17 2024 |
| R-4.3-mac | OK | Sep 17 2024 |
Exports:alltestappendas.data.frameas.dnaas.DNAbinas.listas.matrixas.networkas.networxas.phyDatbasecompboot.dnacalcclustclustersGcontrdistanceext.nodesfillendgapsfillnageodist.corrgroupinghaplohaplotypehapreordhas.cyclehomopolyimageindelcoderindtestncolnrowpairneipairneidistpairPhiSTpairPhiSTdistparsimnetparsnetpegas.amovapielegendpieplotplotpolymorpread.fasrecdistGremove.gapsren.duplirownamesrownames<-showsicsteplimitsubstolowertouppertryconnecttryconnectGuniquevalidityxhaps
Dependencies:apeclicodacpp11digestfansifastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnetworknlmephangornpillarpkgconfigplotrixquadprogRcpprlangsnastatnet.commontibbleutf8vctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony | haplotypes-package haplotypes |
| Extract or replace parts of an object of class 'Dna' | [,Dna,ANY,ANY,ANY-method [,Dna-method [-methods [<-,Dna,ANY,ANY,ANY-method [<-,Dna-method |
| Combines two 'Dna' objects | append,Dna-method append-methods |
| Coerces a 'Dna' object to a data.frame | as.data.frame,Dna-method as.data.frame-methods |
| Coerces an object to a 'Dna' object | as.dna as.dna,character-method as.dna,data.frame-method as.dna,DNAbin-method as.dna,Haplotype-method as.dna,list-method as.dna,matrix-method as.dna,phyDat-method as.dna-methods |
| Coerces an object to a 'DNAbin' object | as.DNAbin as.DNAbin,Dna-method as.DNAbin-methods |
| Methods for function 'as.list' in the Package 'haplotypes' | as.list,Dna-method as.list,Haplotype-method as.list,Parsimnet-method as.list-methods |
| Methods for function 'as.matrix' in the Package 'haplotypes' | as.matrix,Dna-method as.matrix-methods |
| Coerces an object to a 'network' object | as.network as.network,Parsimnet-method as.network-methods |
| Coerces an object to a 'networx' object | as.networx as.networx,Parsimnet-method as.networx-methods |
| Coerces a 'Dna' object to a numeric matrix | as.numeric,Dna-method as.numeric-methods |
| Coerces an object to a 'phyDat' object | as.phyDat as.phyDat,Dna-method as.phyDat-methods |
| Calculates base composition | basecomp basecomp,Dna-method basecomp-methods |
| Generates single bootstrap replicate | boot.dna boot.dna,Dna-method boot.dna-methods |
| Calculates absolute pairwise character difference matrix using a 'Dna' object | distance distance,Dna-method distance-methods |
| Class '"Dna"' in the Package 'haplotypes' | Dna Dna-class |
| Example DNA sequence data | dna.obj |
| Groups haplotypes according to the grouping variable (populations, species, etc.) | grouping grouping,Haplotype-method grouping-methods |
| Class '"Haplotype"' in the Package 'haplotypes' | Haplotype Haplotype-class |
| Methods for function 'haplotype' in the package 'haplotypes' | haplotype haplotype,dist-method haplotype,Dna-method haplotype,matrix-method haplotype-methods |
| Reorders haplotypes according to the ordering factor | hapreord hapreord,Haplotype-method hapreord-methods |
| Provides the list of homoplastic indels and substitutions | homopoly homopoly,Dna-method homopoly-methods |
| Display DNA Sequence | image,Dna-method image-methods |
| Codes gaps | indelcoder indelcoder,Dna-method indelcoder-methods |
| Methods for function 'length' in the package 'haplotypes' | length,Dna-method length,Haplotype-method length,Parsimnet-method length-methods |
| Function to get or set names of a 'Dna' object or 'Parsimnet' object | names,Dna-method names,Parsimnet-method names-methods names<-,Dna-method names<-,Parsimnet-method names<--methods |
| Returns the length of the longest DNA sequence | ncol,Dna-method ncol-methods |
| Returns the number of DNA sequences | nrow,Dna-method nrow-methods |
| Provides the average number of pairwise Nei's (D) differences between populations | pairnei pairnei,dist-method pairnei,Dna-method pairnei,matrix-method pairnei-methods |
| Provides the pairwise PhiST between populations | pairPhiST pairPhiST,dist-method pairPhiST,Dna-method pairPhiST,matrix-method pairPhiST-methods |
| Class '"Parsimnet"' in the Package 'haplotypes' | Parsimnet Parsimnet-class |
| Estimates gene genealogies using statistical parsimony | parsimnet parsimnet,dist-method parsimnet,Dna-method parsimnet,matrix-method parsimnet-methods |
| Add Legends to Plots | pielegend pielegend,Parsimnet,Haplotype-method pielegend-methods |
| Plots pie charts on statistical parsimony network | pieplot pieplot,Parsimnet,Haplotype-method pieplot-methods |
| Methods for function 'plot' in the package 'haplotypes' | plot,Parsimnet,missing-method plot,Parsimnet-method plot-methods |
| Displays polymorphic sites (base substitutions and indels) between two sequences | polymorp polymorp,Dna-method polymorp-methods |
| Returns the minimum and maximum lengths of the DNA sequences | range,Dna-method range-methods |
| Read sequences from a file in FASTA format | read.fas |
| Removing gaps from 'Dna' object | remove.gaps remove.gaps,Dna-method remove.gaps-methods |
| Retrieve or set the row names | rownames,Dna-method rownames,Parsimnet-method rownames-methods rownames<-,Dna-method rownames<-,Parsimnet-method rownames<--methods |
| Methods for function 'show' in the package 'haplotypes' | show,Dna-method show,Haplotype-method show,Parsimnet-method show-methods |
| Displays base substitutions | subs subs,Dna-method subs-methods |
| Convert sequence characters from upper to lower case or vice versa | tolower,Dna-method tolower-methods toupper,Dna-method toupper-methods |
| Extract Unique Sequences | unique,Dna,ANY-method unique,Dna-method unique-methods |
