Class "psam"

Description

An object of class "psam" represents the position specific affinity matrix (PSAM) of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix, which in row i, column j gives the affinity of observing nucleotide/or amino acid i in position j of the motif.

Objects from the Class

Objects can be created by calls of the form new("psam", mat, name, alphabet, color).

Slots

mat

Object of class "matrix" The position specific affinity matrix

name

code"character" The motif name

alphabet

"character" The sequence alphabet. "DNA", "RNA", "AA" or "others".

color

a "character" vector. The color setting for each symbol

Methods

addBlank

signature(x="psam", n="numeric", b="logical") add space into the position specific affinity 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.

coerce

signature(from = "psam", to = "matrix"): convert object psam to matrix

matrixReverseComplement

signature(x = "psam") get the reverse complement of position specific affinity matrix.

plot

signature(x = "psam") Plots the affinity logo of the position specific affinity matrix.

Examples

motif <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
         format="psam")[[1]]
plot(motif)