oligoSummary

0th

Percentile

Output a summary of consensus in the peaks

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

Keywords
misc
Usage
oligoSummary(sequence, oligoLength = 6L, freqs = NULL, MarkovOrder = 3L, quickMotif = FALSE, revcomp=FALSE, maxsize=100000)
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.

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

Aliases
  • oligoSummary
Examples
    if(interactive()){
        data(annotatedPeak)
        library(BSgenome.Hsapiens.UCSC.hg19)
        seq <- getAllPeakSequence(annotatedPeak[1:100], 
                     upstream=20, 
                     downstream=20, 
                     genome=Hsapiens)
        oligoSummary(seq)
    }
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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