This function adds mask 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.
addmask2string(seq, mask = NULL, append = TRUE)DNAStringSet or AAStringSet [mandatory]
IRanges object [mandatory]
indicate if mask should be appended or overwritten [default: TRUE]
An object of class DNAStringSet or AAStringSet
## load example sequence data
data(iupac, package="MSA2dist")
iupac.aa <- iupac |> cds2aa(shorten = TRUE)
## create mask
mask1 <- IRanges::IRanges(start=c(1,41), end=c(20,50))
## add mask
iupac.aa <- iupac.aa |> addmask2string(mask=mask1)
#(iupac.aa |> slot("metadata"))$mask
iupac.aa |> getmask()
#> IRanges object with 2 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 1 20 20
#> [2] 41 50 10
## append mask
mask2 <- IRanges::IRanges(start=c(21), end=c(30))
iupac.aa <- iupac.aa |> addmask2string(mask=mask2)
#(iupac.aa |> slot("metadata"))$mask
iupac.aa |> getmask()
#> IRanges object with 2 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 1 30 30
#> [2] 41 50 10
## overwrite mask
iupac.aa <- iupac.aa |> addmask2string(mask=mask2, append=FALSE)
#(iupac.aa |> slot("metadata"))$mask
iupac.aa |> getmask()
#> IRanges object with 1 range and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 21 30 10
## reduce by mask
#iupac.aa.region <- iupac.aa |> string2region(mask=
# (iupac.aa |> slot("metadata"))$mask)
iupac.aa.region <- iupac.aa |> string2region(mask=
getmask(iupac.aa))
#iupac.aa.region |> slot("metadata")
iupac.aa.region |> getmask()
#> IRanges object with 1 range and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 21 30 10