setMatMatrix: Define the MAT model matrix for an given set of sequences
In steveped/BMEA: Bayesian Modelling for Exon Arrays

Description Usage Arguments Details Value References Examples

Defines the MAT model matrix for a set of sequences.

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setMatMatrix(seq)

setMatVector(seq)

seq

genomic sequences. setMatVector only takes a single string, whilst setMatMatrix takes a vector of strings. Each sequence must be a string of 25 characters containing only the letters A, C, G & T

The function setMatVector is designed for one individual sequence.

Calculates the model matrix for the MAT background model for a given set of genomic sequences. Allows fitting of the MAT model for the purposes of background signal estimation.

setMatVector is designed for internal use only.

setMatMatrix Returns a matrix with nrows=length(seq) & ncol = 80.

setMatVector nReturns a vector of length 80

Kapur, K., Xing, Y., Ouyang, Z., Wong, WH. (2007) Exon arrays provide accurate assessments of gene expression Genome Biol. 8(5):R82

Johnson, W.E., Li, W., Meyer, C.A., Gottardo, R., Carroll, J.S., Brown, M., Liu, X.S. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 103:12457-12462

## Generate a random sequence
seq <- sample(c("A","C","G","T"), 25, replace=TRUE)
seq <- paste(seq,collapse="")
mat.vec <- setMatVector(seq) ## Returns a vector of length 80

## Generate a random sequence
seq <- replicate(2, sample(c("A","C","G","T"), 25, replace=TRUE), simplify = FALSE)
seq <- sapply(seq, paste, collapse = "")
mat.matrix <- setMatMatrix(seq) ## Returns a 2x80 matrix