Careful regularization (pseudocount addition) to a position count matrix.

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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

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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.

Examples

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