psam-methods {motifStack} | R Documentation |
methods for psam objects.
## 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",...)
x |
An object of class |
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 |
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.
signature(x = "psam")
get the
reverse complement of position specific affinity matrix.
signature(x = "psam")
Plots the
affinity logo of the position specific affinity matrix.
Get or set the slot of psam-class
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")