Description Usage Arguments Value References Examples

View source: R/profileScoreDist.R

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.

1 | ```
regularizeMatrix(motif, E = 1.5)
``` |

`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. |

The regularized matrix

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.

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