This MotifSet object is a container for storing the generated motifs from Motif identification softwares, such as MEME.
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A GRangesList. Each GRanges store the starts, ends, strand, seqnames and scores information of one motif sites sequences.
A numeric vector of the E values generated from MEME for each motif.
A DNAStringSet object. It stores the original sequences which are scanned by the software.
MotifSet object is returned.
signature(x = "MotifSet"): Getter
signature(x = "MotifSet")(x, as.prob = FALSE,
shift = 0L, width = NULL, ...):
Calculate the consensus matrix. Other arguments,
please check the
signature(x = "MotifSet"):
Returns the number of motifs.
signature(x = "MotifSet")(x, n=10L, type="none"):
Gets the sites sequences.
n is the number of bases to include from flanking region.
type controls "all", "left", "right" or "none"
flanking sequences are included.
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