psam-class: Class '"psam"'

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

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.

methods for psam objects.

Usage

## S4 method for signature 'psam'
x$name

## S4 method for signature 'psam,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'psam'
matrixReverseComplement(x)

## S4 method for signature 'psam,numeric,logical'
addBlank(x, n, b)

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

## S4 method for signature 'psam'
format(x, ...)

Arguments

x	An object of class psam.
name	Slot name.
y	Not use.
...	Further potential arguments passed to plotAffinityLogo.
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("psam", mat, name, alphabet, color).

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.

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.

$, $<-

Get or set the slot of psam-class

as.data.frame

convert psam-class to a data.frame

format

return the name_pfm of psam-class

Examples

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


motif <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
                      format="psam")[[1]]
matrixReverseComplement(motif)
addBlank(motif, 1, FALSE)
addBlank(motif, 3, TRUE)
as(motif,"matrix")
as.data.frame(motif)
format(motif)

jianhong/motifStack documentation built on Nov. 5, 2024, 7:47 a.m.