# Compute exact position weight/count matrix score distribution.

### Description

Computes the discretisized score distribution of a position count matrix (PCM) or a position weight matrix (PWM), using the method described by Rahmann et al.

### Usage

1 | ```
computeScoreDist(motif, gc, granularity = 0.01, unit = "nat")
``` |

### Arguments

`motif` |
A matrix representing a PCM or PWM; 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. |

`gc` |
A scalar giving the GC fraction to assume. |

`granularity` |
The granularity of the discretization, defaults to 0.01. |

`unit` |
The logarithm unit of the score computed from the PCM or PWM, can be "nat" (default, natural logarithm), "bit" (base 2), or "dit" (base 10). |

### Value

a ProfileDist object

### 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

1 2 3 | ```
data(INR)
thedist <- computeScoreDist(regularizeMatrix(INR), 0.5)
plotDist(thedist)
``` |