addregion2string: addregion2string

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

addregion2string

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

## load example sequence data
data(iupac, package="MSA2dist")
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 |> slot("metadata"))$region
iupac.aa |> region()
## append region
region2 <- IRanges::IRanges(start=c(21), end=c(30))
iupac.aa <- iupac.aa |> addregion2string(region=region2)
#(iupac.aa |> slot("metadata"))$region
iupac.aa |> region()
## overwrite region
iupac.aa <- iupac.aa |> addregion2string(region=region2, append=FALSE)
#(iupac.aa |> slot("metadata"))$region
iupac.aa |> region()
## reduce by region
#iupac.aa.region <- iupac.aa |> string2region(region=
#    (iupac.aa |> slot("metadata"))$region)
iupac.aa.region <- iupac.aa |> string2region(region=
    region(iupac.aa))
#iupac.aa.region |> slot("metadata")
iupac.aa.region |> region()

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