# TFMPvalue-sc2pv: Compute P-value from score. In ge11232002/TFMPvalue: Efficient and Accurate P-Value Computation for Position Weight Matrices

## Description

Computes the P-value associated with a score threshold.

## Usage

 ```1 2``` ```TFMsc2pv(mat, score, bg=c(A=0.25, C=0.25, G=0.25, T=0.25), type=c("PFM", "PWM")) ```

## 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". `score` The required score. `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".

## Value

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

Ge Tan

## References

Touzet, H., and Varre, J.-S. (2007). Efficient and accurate P-value computation for Position Weight Matrices. Algorithms Mol Biol 2, 15.

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10``` ``` 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) score <- 8.77 type <- "PFM" pvalue <- TFMsc2pv(pfm, score, bg, type) ```

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