oligoSummary: Output a summary of consensus in the peaks

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 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)
    }

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