oligoSummary: 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=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

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.

Examples

Run this code

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