addregion2string: addregion2string

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

Description

This function adds region information as an IRanges object, START and END information, to a DNAStringSet or an AAStringSet and puts them into the metadata information. This information can be used to restrict the distance calculation to specific regions of the DNAStringSet or the AAStringSet.

Usage

addregion2string(seq, region = NULL, append = TRUE)

Arguments

seq	DNAStringSet or AAStringSet [mandatory]
region	IRanges object [mandatory]
append	indicate if region should be appended or overwritten [default: TRUE]

Value

An object of class DNAStringSet or AAStringSet

Author(s)

Kristian K Ullrich

See Also

addmask2string, addpop2string, addpos2string

Examples

data(iupac, package="distSTRING")
iupac.aa <- iupac |> cds2aa(shorten = TRUE)
## create region
region1 <- IRanges::IRanges(start=c(1,41), end=c(20,50))
## add region
iupac.aa <- iupac.aa |> addregion2string(region=region1)
iupac.aa@metadata$region
## append region
region2 <- IRanges::IRanges(start=c(21), end=c(30))
iupac.aa <- iupac.aa |> addregion2string(region=region2)
iupac.aa@metadata$region
## overwrite region
iupac.aa <- iupac.aa |> addregion2string(region=region2, append=FALSE)
iupac.aa@metadata$region
## reduce by region
iupac.aa.region <- iupac.aa |> string2region(region=iupac.aa@metadata$region)
iupac.aa.region@metadata

kullrich/distSTRING documentation built on Dec. 21, 2021, 8:42 a.m.