regularizeMatrix: Careful regularization (pseudocount addition) to a position count matrix.
Description
Carries out the regularization suggested by Rahmann et al. This lets each
column in the regularized matrix be a linear combination of the column in the
non-regularized matrix and rho, the overall base distribution of all
positions. The weighting of the linear combination is determined by the
parameter E in a non-trivial way, see Rahmann et al. for more information. A
default value E=1.5 usually works well.
Usage
regularizeMatrix(motif, E = 1.5)
Arguments
motif
A position count matrix; each column a position and each row a
base corresponding to A, C, G, T. This order is assumed, unless the rows
are correspondingly named in a different order.
E
Weighting parameter between 0 and 3 for the regularization.
Value
The regularized matrix
References
Rahmann, S., Mueller, T., and Vingron, M. (2003). On the power of
profiles for transcription factor binding site detection. Stat Appl Genet
Mol Biol 2, Article7.