An object of class "pcm" represents the position count
matrix of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix,
which in row i, column j gives the
counts of observing nucleotide/or amino acid i in
position j of the motif.
Objects from the Class
Objects can be created by calls of the form new("pcm", mat, name, alphabet, color, background).
Slots
mat
Object of class "matrix" The position count matrix
name
code"character" The motif name
alphabet
"character" The sequence
alphabet. "DNA", "RNA", "AA" or "others".
color
a "character" vector. The color setting for each symbol
background
a "numeric" vector. The background frequency.
Methods
addBlank
signature(x="pcm", n="numeric", b="logical") add space
into the position count 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.
coerce
signature(from = "pcm", to = "matrix"): convert object pcm to matrix
getIC
signature(x = "pcm",) Calculate information
content profile for position frequency matrix.
matrixReverseComplement
signature(x = "pcm") get the
reverse complement of position frequency matrix.
trimMotif
signature(x = "pcm", t= "numeric") trim motif by information content.
plot
signature(x = "pcm") Plots the
sequence logo of the position count matrix.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> library(motifStack)
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: MotIV
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Attaching package: 'MotIV'
The following object is masked from 'package:stats':
filter
Loading required package: ade4
Attaching package: 'ade4'
The following object is masked from 'package:BiocGenerics':
score
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/motifStack/pcm-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pcm-class
> ### Title: Class '"pcm"'
> ### Aliases: pcm-class
> ### Keywords: classes
>
> ### ** 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 <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")
> plot(motif)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.