ChIPpeakAnno (version 2.16.4)

countPatternInSeqs: Output total number of patterns found in the input sequences

Description

Output total number of patterns found in the input sequences

Usage

countPatternInSeqs(pattern, sequences)

Arguments

pattern

DNAstringSet object

sequences

a vector of sequences

Value

Total number of occurrence of the pattern in the sequences

Details

References

See Also

summarizePatternInPeaks, translatePattern

Examples

	filepath = system.file("extdata", "examplePattern.fa", package="ChIPpeakAnno")
	dict = readDNAStringSet(filepath = filepath, format="fasta", use.names=TRUE)
	sequences = c("ACTGGGGGGGGCCTGGGCCCCCAAAT", "AAAAAACCCCTTTTGGCCATCCCGGGACGGGCCCAT", "ATCGAAAATTTCC")
	countPatternInSeqs(pattern=dict[1], sequences=sequences)
	countPatternInSeqs(pattern=dict[2], sequences=sequences)
	pattern = DNAStringSet("ATNGMAA")
	countPatternInSeqs(pattern=pattern, sequences=sequences)