DNA.dist: Matrix of DNA distances given an alignment
In QSutils: Quasispecies Diversity

Description Usage Arguments Value Author(s) References See Also Examples

Function to compute a matrix of pairwise distances from DNA sequences using a model of DNA evolution. It relies on the dist.dna() function in the APE package.

1	DNA.dist(seqs, model = "raw", gamma = FALSE, pairwise.deletion = FALSE)

`seqs`	DNAStringSet object with the aligned haplotypes.
`model`	Evolutionary model to compute genetic distance by default "raw", but "N", "TS", "TV", "JC69", "K80", "F81", "K81", "F84", "BH87", "T92","TN93", "GG95", "logdet", "paralin", "indel", or "indelblock" can also be used.
`gamma`	Gamma parameter possibly used to apply a correction to the distances or FALSE (by default).
`pairwise.deletion`	A logical indicating whether to delete sites with missing data (gaps) in a pairwise manner. The default is to delete sites with at least one missing datum in all sequences.

Object of class "dist" with pairwise distances.

Mercedes Guerrero-Murillo and Josep Gregori

Paradis E., Claude J. and Strimmer K., APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 2004, 20, 289-290

Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.

Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.

dist.dna

filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")

dst <- DNA.dist(lst$hseqs,model="N")
dst

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

                    Hpl_0_0001|464|46.4 Hpl_1_0001|62|6.2 Hpl_1_0002|39|3.9
Hpl_1_0001|62|6.2                     1                                    
Hpl_1_0002|39|3.9                     1                 2                  
Hpl_1_0003|27|2.7                     1                 2                 2
Hpl_2_0001|37|3.7                     2                 1                 3
Hpl_4_0001|16|1.6                     4                 3                 5
Hpl_5_0001|33|3.3                     5                 4                 6
Hpl_8_0001|54|5.4                     8                 7                 9
Hpl_9_0001|248|24.8                   9                 8                10
Hpl_10_0001|20|2                     10                 9                11
                    Hpl_1_0003|27|2.7 Hpl_2_0001|37|3.7 Hpl_4_0001|16|1.6
Hpl_1_0001|62|6.2                                                        
Hpl_1_0002|39|3.9                                                        
Hpl_1_0003|27|2.7                                                        
Hpl_2_0001|37|3.7                   3                                    
Hpl_4_0001|16|1.6                   5                 4                  
Hpl_5_0001|33|3.3                   6                 5                 5
Hpl_8_0001|54|5.4                   9                 8                 8
Hpl_9_0001|248|24.8                 8                 9                 9
Hpl_10_0001|20|2                    9                10                10
                    Hpl_5_0001|33|3.3 Hpl_8_0001|54|5.4 Hpl_9_0001|248|24.8
Hpl_1_0001|62|6.2                                                          
Hpl_1_0002|39|3.9                                                          
Hpl_1_0003|27|2.7                                                          
Hpl_2_0001|37|3.7                                                          
Hpl_4_0001|16|1.6                                                          
Hpl_5_0001|33|3.3                                                          
Hpl_8_0001|54|5.4                   3                                      
Hpl_9_0001|248|24.8                 4                 1                    
Hpl_10_0001|20|2                    5                 2                   1