costMatrix: Segmentation cost matrix
In tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

Description Usage Arguments Details Value Author(s) Examples

This function calculates the cost matrix for the segmentation model

1	costMatrix(x, maxk)

`x`	Numeric vector of length `n` or matrix with `n` rows and `d` columns, where `n` is the number of sample points and `d` the number of replicate measurements (e.g. from multiple arrays).
`maxk`	Positive integer.

See the package vignette Calculation of the cost matrix.

Matrix with maxk rows and length(x) columns.

W. Huber

d = 4
x = apply(matrix(rnorm(200), ncol=d), 2, cumsum)
maxk = 50
 
G = costMatrix(x, maxk=maxk)
 
G.pedestrian = matrix(NA, nrow=nrow(G), ncol=ncol(G))
for(i in 1:(ncol(G)))
  for(k in 1:min(nrow(G), nrow(x)-i+1))
    G.pedestrian[k, i] = (k*d-1)*var(as.vector(x[i:(i+k-1), ]))
 
stopifnot(identical(is.na(G), is.na(G.pedestrian)))
stopifnot(max(abs(G-G.pedestrian), na.rm=TRUE) <= 1e-6)