isPatternUnique: Output whether the input patterns occurs only once in the...

In LihuaJulieZhu/CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

Output whether the input patterns occurs only once in the sequence

Description

Input a sequence and a list of patterns and determine if the patterns occurs only once in the sequence. Used for determining whether an RE site in gRNA also occurs in the flanking region.

Usage

isPatternUnique(seq, patterns)

Arguments

seq	flanking sequence of a gRNA
patterns	patterns as DNAStringSet, such as a list of RE sites

Value

returns a character vectors containing the uniqueness of each pattern/RE site

Author(s)

Lihua Julie Zhu

Examples

    seq <- "TGGATTGTATAATCAGCATGGATTTGGAAC"
    patterns <- DNAStringSet(c("TGG", "TGGA", "TGGATA", "TTGGAAC", ""))
    isPatternUnique(seq, patterns)
    isPatternUnique(seq)
    isPatternUnique(patterns)

LihuaJulieZhu/CRISPRseek documentation built on Feb. 3, 2024, 2:44 p.m.