psam-class {motifStack} | R Documentation |
"psam"
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.
## 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, ...)
x |
An object of class |
name |
Slot name. |
y |
Not use. |
... |
Further potential arguments passed to |
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 can be created by calls of the form
new("psam", mat, name, alphabet, color)
.
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
convert psam-class
to a data.frame
return the name_pfm of psam-class
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)