subString: subString

In kullrich/distSTRING: distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Description

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

Usage

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

Author(s)

Kristian K Ullrich

See Also

subseq

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))

kullrich/distSTRING documentation built on Dec. 21, 2021, 8:42 a.m.