psam-methods {motifStack}R Documentation

"psam" methods

Description

methods for psam objects.

Usage

	## S4 method for signature 'psam,numeric,logical'
addBlank(x,n,b)
	## S4 method for signature 'psam'
matrixReverseComplement(x)
	## S4 method for signature 'psam,ANY'
plot(x,y="missing",...)

Arguments

x

An object of class psam.

y

Not use.

n

how many spaces should be added.

b

logical value to indicate where the space should be added.

...

Further potential arguments passed to plotAffinityLogo.

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

Examples

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")

[Package motifStack version 1.28.0 Index]