An object of class
"pfm" represents the position frequency
matrix of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix,
which in row i, column j gives the
frequency of observing nucleotide/or amino acid i in
position j of the motif.
Objects can be created by calls of the form
new("pfm", mat, name, alphabet, color, background).
Object of class
"matrix" The position frequency 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="pfm", n="numeric", b="logical") add space
into the position frequency 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 = "pfm", to = "matrix"): convert object pfm to matrix
signature(x = "pfm",) Calculate information
content profile for position frequency matrix.
signature(x = "matrix", p = "numeric") Calculate
information content profile for matrix. p is the background frequency
signature(x = "pfm") get the
reverse complement of position frequency matrix.
signature(x = "pfm", t= "numeric") trim motif by information content.
signature(x = "pfm") Plots the
sequence logo of the position frequency matrix.
1 2 3 4 5 6
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.