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

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

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

Author(s)

Lihua Julie Zhu

See Also

summarizePatternInPeaks, translatePattern

Examples

  library(Biostrings)
  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)

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.