addregion2string

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.

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

See also

addmask2string, addpop2string, addpos2string

Author

Kristian K Ullrich

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"))$region
iupac.aa |> region()
#> IRanges object with 2 ranges and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]         1        20        20
#>   [2]        41        50        10
## append region
region2 <- IRanges::IRanges(start=c(21), end=c(30))
iupac.aa <- iupac.aa |> addregion2string(region=region2)
#(iupac.aa |> slot("metadata"))$region
iupac.aa |> region()
#> IRanges object with 2 ranges and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]         1        30        30
#>   [2]        41        50        10
## overwrite region
iupac.aa <- iupac.aa |> addregion2string(region=region2, append=FALSE)
#(iupac.aa |> slot("metadata"))$region
iupac.aa |> region()
#> IRanges object with 1 range and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]        21        30        10
## reduce by region
#iupac.aa.region <- iupac.aa |> string2region(region=
#    (iupac.aa |> slot("metadata"))$region)
iupac.aa.region <- iupac.aa |> string2region(region=
    region(iupac.aa))
#iupac.aa.region |> slot("metadata")
iupac.aa.region |> region()
#> IRanges object with 1 range and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]        21        30        10