psam-class {motifStack} | R Documentation |
"psam"
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 can be created by calls of the form new("psam", mat, name, alphabet, color)
.
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
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.
signature(from = "psam", to = "matrix")
: convert object psam to matrix
signature(x = "psam")
get the
reverse complement of position specific affinity matrix.
signature(x = "psam")
Plots the
affinity logo of the position specific affinity matrix.
motif <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), format="psam")[[1]] plot(motif)