countPatternInSeqs {ChIPpeakAnno} | R Documentation |
Output total number of patterns found in the input sequences
countPatternInSeqs(pattern, sequences)
pattern |
DNAstringSet object |
sequences |
a vector of sequences |
Total number of occurrence of the pattern in the sequences
Lihua Julie Zhu
summarizePatternInPeaks, translatePattern
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)