toICM-methods: toICM method
In ge11232002/TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

Converts a raw frequency matrix (PFMatrix) to a information content matrix (ICMatrix). It takes the bases background frequencies, pseudocounts and schneider as parameters.

1 2	toICM(x, pseudocounts=0.8, schneider=FALSE, bg=c(A=0.25, C=0.25, G=0.25, T=0.25))

`x`	For `toPWM`, a PFMatrix, rectangular DNAStringSet object ("rectangular" means that all elements have the same number of characters) with no IUPAC ambiguity letters, a rectangular character vector or a matrix with rownames containing at least A, C, G and T, or a PFMatrixList object
`pseudocounts`	A default value 0.8 is used.
`schneider`	This logical parameter controls whether a Schneider correction will be done. See more details below.
`bg`	bg is a vector of background frequencies of four bases with names containing A, C, G, T. When toPWM is applied to a `PFMatrix`, if bg is not specified, it will use the bg information contained in `PFMatrix`.

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

D = log2(nrow(pfm)) + colSums(postProbs * log2(postProbs))

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.

A ICMatrix object which contains the background frequency, pseudocounts and Schneider correction used.

Ge Tan

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.

toPWM, XMatrix, seqLogo

  ## 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)