aastring2dist: aastring2dist

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

aastring2dist

Description

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

Usage

aastring2dist(
  aa,
  threads = 1,
  symmetric = TRUE,
  score = NULL,
  mask = NULL,
  region = NULL
)

Arguments

aa	AAStringSet [mandatory]
threads	number of parallel threads [default: 1]
symmetric	symmetric score matrix [default: TRUE]
score	score matrix use a score matrix to calculate distances [mandatory]
mask	IRanges object indicating masked sites [default: NULL]
region	IRanges object indicating region to use for dist calculation (by default all sites are used) [default: NULL]

Value

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

Author(s)

Kristian K Ullrich

See Also

dnastring2dist

Examples

## load example sequence data
data("hiv", package="MSA2dist")
#aastring2dist(cds2aa(hiv), score=granthamMatrix())
hiv |> cds2aa() |> aastring2dist(score=granthamMatrix())
## create mask
mask1 <- IRanges::IRanges(start=c(11,41,71), end=c(20,50,80))
## use mask
hiv |> cds2aa() |> aastring2dist(score=granthamMatrix(), mask=mask1)
## use region
region1 <- IRanges::IRanges(start=c(1,75), end=c(45,85))
hiv |> cds2aa() |> aastring2dist(score=granthamMatrix(), region=region1)
## use mask and region
hiv |> cds2aa() |> aastring2dist(score=granthamMatrix(),
    mask=mask1, region=region1)
## use asymmetric score matrix
myscore <- granthamMatrix()
myscore[5, 6] <- 0
h <- hiv |> cds2aa() |> aastring2dist(score=myscore, symmetric=FALSE)
h$distSTRING[1:2, 1:2]

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