DNASuffixArray {Biostrings} | R Documentation |
This function creates a suffix array for the given DNA strings. The sorting of the suffix array can be done based on a given number of letters at the begining of each suffix.
DNASuffixArray(x, prefixLength = max(nchar(x)))
x |
an objecct of class "BioString" representing one or more DNA strings. If its length is more than one, suffix arrays for each of the string are created and merged. |
prefixLength |
the number of letters at the begining of each suffix that are used in sorting the suffix array. |
An object of class "BioString", with the suffixes from the argument sorted in increasing order. For the purpose of sorting, each string is assumed to be padded at the end with a letter lower in order than any letter in the alphabet of the string.
Saikat DebRoy
sortDNAString
for sorting the strings in an
object of class "BioString".
data('yeastSEQCHR1') yeast1 <- DNAString(yeastSEQCHR1) DNASuffixArray(substr(yeast1, 1, 30)) x <- substring(yeast1, c(1, 16), c(15, 30)) x DNASuffixArray(x)