An object of class
"pcm" represents the position count
matrix of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix,
which in row i, column j gives the
counts of observing nucleotide/or amino acid i in
position j of the motif.
Objects can be created by calls of the form
new("pcm", mat, name, alphabet, color, background).
Object of class
"matrix" The position count matrix
code"character" The motif name
"character" The sequence
alphabet. "DNA", "RNA", "AA" or "others".
"character" vector. The color setting for each symbol
"numeric" vector. The background frequency.
signature(x="pcm", n="numeric", b="logical") add space
into the position count matrix for alignment. b is a bool value, if TRUE, add
space to the 3' end, else add space to the 5' end. n indicates how many
spaces should be added.
signature(from = "pcm", to = "matrix"): convert object pcm to matrix
signature(x = "pcm",) Calculate information
content profile for position frequency matrix.
signature(x = "pcm") get the
reverse complement of position frequency matrix.
signature(x = "pcm", t= "numeric") trim motif by information content.
signature(x = "pcm") Plots the
sequence logo of the position count matrix.
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