string2region: string2region

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

string2region

Description

This function subsets a DNAStringSet or an AAStringSet by a mask and region given one or both options as IRanges.

Usage

string2region(seq, mask = NULL, region = NULL, add = TRUE)

Arguments

seq	DNAStringSet or AAStringSet [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]
add	indicate if mask and region should be added to metadata [default: TRUE]

Value

A list object with the following components:
DNAStringSet or AAStringSet
regionUsed

Author(s)

Kristian K Ullrich

See Also

dnastring2dist

Examples

## load example sequence data
data("hiv", package="MSA2dist")
## create mask
mask1 <- IRanges::IRanges(start=c(11,41,71), end=c(20,50,80))
## use mask
hiv.region <- hiv |> cds2aa() |> string2region(mask=mask1)
#(hiv.region |> slot("metadata"))$regionUsed
hiv.region |> regionused()
## use region
region1 <- IRanges::IRanges(start=c(1,75), end=c(45,85))
hiv.region <- hiv |> cds2aa() |> string2region(region=region1)
#(hiv.region |> slot("metadata"))$regionUsed
hiv.region |> regionused()
## use mask and region
hiv.region <- hiv |> cds2aa() |> string2region(mask=mask1, region=region1)
#(hiv.region |> slot("metadata"))$regionUsed
hiv.region |> regionused()

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