dnastring2dist: dnastring2dist

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

dnastring2dist

Description

This function calculates pairwise distances for all combinations of a DNAStringSet.

Usage

dnastring2dist(
  dna,
  model = "IUPAC",
  threads = 1,
  symmetric = TRUE,
  score = NULL,
  mask = NULL,
  region = NULL,
  ...
)

Arguments

dna	DNAStringSet [mandatory]
model	specify model either "IUPAC" or any model from ape::dist.dna [default: IUPAC]
threads	number of parallel threads [default: 1]
symmetric	symmetric score matrix [default: TRUE]
score	score matrix use score matrix to calculate distances [default: NULL]
mask	IRanges object indicating masked sites [default: NULL]
region	IRanges object indicating region to use for dist calculation. Default is null, meaning all sites are used [default: NULL]
...	other ape::dist.dna parameters (see dist.dna)

Value

A data.frame of pairwise distance values distSTRING and sites used sitesUsed

Author(s)

Kristian K Ullrich

See Also

dist.dna

Examples

## load example sequence data
data("hiv", package="MSA2dist")
#dnastring2dist(hiv, model="IUPAC")
hiv |> dnastring2dist(model="IUPAC")
#dnastring2dist(hiv, model="K80")
hiv |> dnastring2dist(model="K80")
data("woodmouse", package="ape")
#dnastring2dist(dnabin2dnastring(woodmouse), score=iupacMatrix())
woodmouse |> dnabin2dnastring() |> dnastring2dist()
#dnastring2dist(hiv, model = "IUPAC", threads = 2)
hiv |> dnastring2dist(model = "IUPAC", threads = 2)
## create mask
mask1 <- IRanges::IRanges(start=c(1,61,121), end=c(30,90,150))
## use mask
hiv |> dnastring2dist(model="IUPAC", mask=mask1)
## use region
region1 <- IRanges::IRanges(start=c(1,139), end=c(75,225))
hiv |> dnastring2dist(model="IUPAC", region=region1)
## use mask and region
hiv |> dnastring2dist(model="IUPAC", mask=mask1, region=region1)
## use asymmetric score matrix
myscore <- iupacMatrix()
myscore[1, 4] <- 0.5
(hiv |> dnastring2dist(score=myscore, symmetric=FALSE))$distSTRING[1:2, 1:2]

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.