motifStack (version 1.16.2)

pfm-class: Class "pfm"

Description

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 from the Class

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

Examples

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)