This function subsets a DNAStringSet
or an
AAStringSet
by a mask
and region
given one or both
options as IRanges
.
string2region(seq, mask = NULL, region = NULL, add = TRUE)
DNAStringSet
or AAStringSet
[mandatory]
IRanges
object indicating masked sites [default: NULL]
IRanges
object indicating region to use for dist
calculation (by default all sites are used) [default: NULL]
indicate if mask and region should be added to metadata
[default: TRUE]
A list
object with the following components:
DNAStringSet
or AAStringSet
regionUsed
## 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"))$regionUsed
hiv.region |> regionused()
#> IRanges object with 4 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 1 10 10
#> [2] 21 40 20
#> [3] 51 70 20
#> [4] 81 91 11
## use region
region1 <- IRanges::IRanges(start=c(1,75), end=c(45,85))
hiv.region <- hiv |> cds2aa() |> string2region(region=region1)
#(hiv.region |> slot("metadata"))$regionUsed
hiv.region |> regionused()
#> IRanges object with 2 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 1 45 45
#> [2] 75 85 11
## use mask and region
hiv.region <- hiv |> cds2aa() |> string2region(mask=mask1, region=region1)
#(hiv.region |> slot("metadata"))$regionUsed
hiv.region |> regionused()
#> IRanges object with 3 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 1 10 10
#> [2] 21 40 20
#> [3] 81 85 5