oligoSummary {ChIPpeakAnno} | R Documentation

## Output a summary of consensus in the peaks

### Description

Calculate the z-scores of all combinations of oligonucleotide in a given length by Markove chain.

### Usage

    oligoSummary(
      sequence,
      oligoLength = 6L,
      freqs = NULL,
      MarkovOrder = 3L,
      quickMotif = FALSE,
      revcomp = FALSE,
      maxsize = 1e+05
    )

### Arguments

`sequence` | The sequences packaged in DNAStringSet, DNAString object or output of function getAllPeakSequence.
`oligoLength` | The length of oligonucleotide.
`freqs` | Output of function frequency.
`MarkovOrder` | The order of Markov chain.
`quickMotif` | Generate the motif by z-score of not.
`revcomp` | Consider both the given strand and the reverse complement strand when searching for motifs in a complementable alphabet (ie DNA). Default, FALSE.
`maxsize` | Maximum allowed dataset size (in length of sequences).

### Value

A list is returned.

`zscore` | A numeric vector. The z-scores of each oligonucleotide.
`counts` | A numeric vector. The counts number of each oligonucleotide.
`motifs` | a list of motif matrix.

### Author(s)

Jianhong Ou

### References

van Helden, Jacques, Marcel li del Olmo, and Jose E. Perez-Ortin. "Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals." Nucleic Acids Research 28.4 (2000): 1000-1010.

### See Also

See Also as `frequency`

### Examples

        if(interactive() || Sys.getenv("USER")=="jianhongou"){
            data(annotatedPeak)
            library(BSgenome.Hsapiens.UCSC.hg19)
            library(seqinr)
            seq <- getAllPeakSequence(annotatedPeak[1:100],
                         upstream=20,
                         downstream=20,
                         genome=Hsapiens)
            oligoSummary(seq)
        }

[Package ChIPpeakAnno version 3.24.2 Index]