translatePattern: translate pattern from IUPAC Extended Genetic Alphabet to...

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

translate pattern from IUPAC Extended Genetic Alphabet to regular expression

Description

translate pattern containing the IUPAC nucleotide ambiguity codes to regular expression. For example,Y->[C|T], R-> [A|G], S-> [G|C], W-> [A|T], K-> [T|U|G], M-> [A|C], B-> [C|G|T], D-> [A|G|T], H-> [A|C|T], V-> [A|C|G] and N-> [A|C|T|G].

Usage

translatePattern(pattern)

Arguments

pattern

a character vector with the IUPAC nucleotide ambiguity codes

Value

a character vector with the pattern represented as regular expression

Author(s)

Lihua Julie Zhu

See Also

countPatternInSeqs, summarizePatternInPeaks

Examples

    pattern1 = "AACCNWMK"
    translatePattern(pattern1)

jianhong/ChIPpeakAnno documentation built on April 28, 2024, 3:10 p.m.