pfm-class {motifStack} | R Documentation |
"pfm"
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)
.
mat
Object of class "matrix"
The position frequency 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
background
a "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.
pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm")) pcm <- pcm[,3:ncol(pcm)] rownames(pcm) <- c("A","C","G","T") motif <- pcm2pfm(pcm) motif <- new("pfm", mat=motif, name="bin_SOLEXA") plot(motif)