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

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

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)

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.