subString

This function gets a subsequence from a DNAString, RNAString, AAString, BString, DNAStringSet, RNAStringSet, AAStringSet, BStringSet object from the Biostrings package.

subString(x, s, e)

Arguments

x

DNAStringSet, RNAString, AAString, BString, DNAStringSet, RNAStringSet, AAStringSet, BStringSet [mandatory]

s

start vector [mandatory]

e

end vector [mandatory]

Value

subsequence of an Biostrings object

See also

subseq

Author

Kristian K Ullrich

Examples

## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
    Biostrings::DNAStringSet(cds2))
subString(cds1.cds2.aln, c(1,7), c(3,12))
#> DNAStringSet object of length 2:
#>     width seq
#> [1]     9 ATGCATTGC
#> [2]     9 ATGCATTGC