# TFMPvalue-lazyScore: Compute the score from P-value. In ge11232002/TFMPvalue: Efficient and Accurate P-Value Computation for Position Weight Matrices

## Description

Computes the score threshold associated with P-value p using the algorithm of Beckstette 2006.

## Usage

 ```1 2``` ```TFMLazyScore(mat, pvalue, bg=c(A=0.25, C=0.25, G=0.25, T=0.25), type=c("PFM", "PWM"), granularity=1e-5) ```

## Arguments

 `mat` The input matrix. It can be a Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) in log ratio. The matrix must have row names with "A", "C", "G", "T". `pvalue` The required P-value. `bg` The background frequency of the sequences. A numeric vector with names "A", "C", "G", "T". `type` The type of input matrix. Can be "PFM" or "PWM". `granularity` The granularity used in the computation.

## Value

The score is returned based on the matrix, given P-value and granularity.

Ge Tan

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14``` ``` ## This example is not tested due to running time > 5s pfm <- matrix(c(3, 5, 4, 2, 7, 0, 3, 4, 9, 1, 1, 3, 3, 6, 4, 1, 11, 0, 3, 0, 11, 0, 2, 1, 11, 0, 2, 1, 3, 3, 2, 6, 4, 1, 8, 1, 3, 4, 6, 1, 8, 5, 1, 0, 8, 1, 4, 1, 9, 0, 2, 3, 9, 5, 0, 0, 11, 0, 3, 0, 2, 7, 0, 5), nrow = 4, dimnames = list(c("A","C","G","T")) ) bg <- c(A=0.25, C=0.25, G=0.25, T=0.25) pvalue <- 1e-5 type <- "PFM" granularity <- 1e-5 TFMLazyScore(pfm, pvalue, bg, type, granularity) ```

ge11232002/TFMPvalue documentation built on May 17, 2019, 12:13 a.m.