Class "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.

methods for pfm objects.

# S4 method for pfm
$(x, name)

# S4 method for pfm,ANY
plot(x, y = "missing", ...)

# S4 method for pfm,ANY
getIC(x, p = "missing")

# S4 method for pfm,numeric
trimMotif(x, t)

# S4 method for pfm
matrixReverseComplement(x)

# S4 method for pfm,numeric,logical
addBlank(x, n, b)

# S4 method for pfm
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

# S4 method for pfm
format(x, ...)

Arguments

x	An object of class pfm. For getIC, if parameter p is followed, x should be an object of matrix.
name	Slot name.
y	Not use.
...	Further potential arguments passed to plotMotifLogo.
p	p is the background frequency.
t	numeric value of information content threshold for trimming.
n	how many spaces should be added.
b	logical value to indicate where the space should be added.
row.names, optional	see as.data.frame

Objects from the Class

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

Methods

addBlank

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.

getIC

signature(x = "pfm",) Calculate information content profile for position frequency matrix.

getIC

signature(x = "matrix", p = "numeric") Calculate information content profile for matrix. p is the background frequency

matrixReverseComplement

signature(x = "pfm") get the reverse complement of position frequency matrix.

plot

signature(x = "pfm") Plots the sequence logo of the position frequency matrix.

trimMotif

signature(x = "pfm", t= "numeric") trim motif by information content.

$, $<-

Get or set the slot of pfm-class

as.data.frame

convert pfm-class to a data.frame

format

return the name_pfm of pfm-class

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)


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")
getIC(motif)
#>        V3        V4        V5        V6        V7        V8        V9 
#> 0.5575323 1.6879104 2.0000000 1.7166385 2.0000000 1.5886941 1.7313686 
matrixReverseComplement(motif)
#> An object of class "pfm"
#> Slot "mat":
#>         [,1]       [,2] [,3]       [,4] [,5]       [,6]       [,7]
#> A 0.04588015 0.05898876    0 0.01779026    0 0.94382022 0.02902622
#> C 0.00000000 0.01123596    0 0.00000000    0 0.00000000 0.47191011
#> G 0.00000000 0.92977528    0 0.02247191    0 0.05617978 0.06647940
#> T 0.95411985 0.00000000    1 0.95973783    1 0.00000000 0.43258427
#> 
#> Slot "name":
#> [1] "bin_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
addBlank(motif, 1, FALSE)
#> An object of class "pfm"
#> Slot "mat":
#>                V3         V4 V5         V6 V7         V8         V9
#> A 0.25 0.43258427 0.00000000  1 0.95973783  1 0.00000000 0.95411985
#> C 0.25 0.06647940 0.05617978  0 0.02247191  0 0.92977528 0.00000000
#> G 0.25 0.47191011 0.00000000  0 0.00000000  0 0.01123596 0.00000000
#> T 0.25 0.02902622 0.94382022  0 0.01779026  0 0.05898876 0.04588015
#> 
#> Slot "name":
#> [1] "bin_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
addBlank(motif, 3, TRUE)
#> An object of class "pfm"
#> Slot "mat":
#>           V3         V4 V5         V6 V7         V8         V9               
#> A 0.43258427 0.00000000  1 0.95973783  1 0.00000000 0.95411985 0.25 0.25 0.25
#> C 0.06647940 0.05617978  0 0.02247191  0 0.92977528 0.00000000 0.25 0.25 0.25
#> G 0.47191011 0.00000000  0 0.00000000  0 0.01123596 0.00000000 0.25 0.25 0.25
#> T 0.02902622 0.94382022  0 0.01779026  0 0.05898876 0.04588015 0.25 0.25 0.25
#> 
#> Slot "name":
#> [1] "bin_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
as(motif,"matrix")
#>           V3         V4 V5         V6 V7         V8         V9
#> A 0.43258427 0.00000000  1 0.95973783  1 0.00000000 0.95411985
#> C 0.06647940 0.05617978  0 0.02247191  0 0.92977528 0.00000000
#> G 0.47191011 0.00000000  0 0.00000000  0 0.01123596 0.00000000
#> T 0.02902622 0.94382022  0 0.01779026  0 0.05898876 0.04588015
as.data.frame(motif)
#>           V3         V4 V5         V6 V7         V8         V9
#> A 0.43258427 0.00000000  1 0.95973783  1 0.00000000 0.95411985
#> C 0.06647940 0.05617978  0 0.02247191  0 0.92977528 0.00000000
#> G 0.47191011 0.00000000  0 0.00000000  0 0.01123596 0.00000000
#> T 0.02902622 0.94382022  0 0.01779026  0 0.05898876 0.04588015
format(motif)
#> [1] "bin_SOLEXA_pfm"