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\name{toICM}
\docType{methods}
\alias{toICM}
\alias{toICM,character-method}
\alias{toICM,DNAStringSet-method}
\alias{toICM,matrix-method}
\alias{toICM,PFMatrix-method}
\alias{toICM,PFMatrixList-method}
\title{toICM method}
\description{
Converts a raw frequency matrix (PFMatrix) to a information content matrix (ICMatrix).
It takes the bases background frequencies, pseudocounts and
schneider as parameters.
}
\usage{
toICM(x, pseudocounts=0.8, schneider=FALSE,
bg=c(A=0.25, C=0.25, G=0.25, T=0.25))
}
\arguments{
\item{x}{
For \code{toPWM}, a \link{PFMatrix},
rectangular \link{DNAStringSet} object ("rectangular" means that
all elements have the same number of characters) with
no IUPAC ambiguity letters,
a rectangular \link{character} vector or
a \link{matrix} with rownames containing at least A, C, G and T,
or a \link{PFMatrixList} object
}
\item{pseudocounts}{
A default value 0.8 is used.
}
\item{schneider}{
This logical parameter controls whether a Schneider correction will be done.
See more details below.
}
\item{bg}{
bg is a vector of background frequencies of four bases with names containing A, C, G, T. When toPWM is applied to a \code{PFMatrix}, if bg is not specified, it will use the bg information contained in \code{PFMatrix}.
}
}
\details{
The information content matrix has a column sum between 0 (no base preference) and 2 (only 1 base used). Usually this information is used to plot sequence log.
The information content at each position is computed
\deqn{D = \log_2(nrow(pfm)) + colSums(postProbs \times \log_2(postProbs)}{%
D = log2(nrow(pfm)) + colSums(postProbs * log2(postProbs))}
\deqn{icm = posProbs * D}
where D is the total information contect for each position.
For detailed procedure of computation, please refer to the vignette.
If a Schneider correction will be done if requested.
Please see the reference below for more comprehensive explanation.
}
\value{
A \code{ICMatrix} object which contains the background frequency,
pseudocounts and Schneider correction used.
}
\references{
Schneider, T. D., Stormo, G. D., Gold, L., & Ehrenfeucht, A. (1986). Information content of binding sites on nucleotide sequences. Journal of molecular biology, 188(3), 415-431.
}
\author{
Ge Tan
}
\seealso{
\code{\link{toPWM}},
\code{\linkS4class{XMatrix}},
\code{\link{seqLogo}}
}
\examples{
## Constructor a PFMatrix
pfm <- PFMatrix(ID="MA0004.1", name="Arnt", matrixClass="Zipper-Type",
strand="+",
bg=c(A=0.25, C=0.25, G=0.25, T=0.25),
tags=list(family="Helix-Loop-Helix",
species="10090",
tax_group="vertebrates",
medline="7592839", type="SELEX", ACC="P53762",
pazar_tf_id="TF0000003",
TFBSshape_ID="11", TFencyclopedia_ID="580"),
profileMatrix=matrix(c(4L, 19L, 0L, 0L, 0L, 0L,
16L, 0L, 20L, 0L, 0L, 0L,
0L, 1L, 0L, 20L, 0L, 20L,
0L, 0L, 0L, 0L, 20L, 0L),
byrow=TRUE, nrow=4,
dimnames=list(c("A", "C", "G", "T")))
)
## Convert it into a PWMatrix
icm <- toICM(pfm, pseudocounts=0.8, schneider=TRUE)
## Conversion on PWMatrixList
data(MA0003.2)
data(MA0004.1)
pfmList <- PFMatrixList(pfm1=MA0003.2, pfm2=MA0004.1, use.names=TRUE)
icmList <- toICM(pfmList, pseudocounts=0.8, schneider=TRUE)
}
\keyword{methods}
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