oligoSummary {ChIPpeakAnno} | R Documentation |
Calculate the z-scores of all combinations of oligonucleotide in a given length by Markove chain.
oligoSummary( sequence, oligoLength = 6L, freqs = NULL, MarkovOrder = 3L, quickMotif = FALSE, revcomp = FALSE, maxsize = 1e+05 )
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). |
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. |
Jianhong Ou
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 as frequency
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) }