R: Compute P-value from score.

TFMsc2pv {TFMPvalue} | R Documentation

## Compute P-value from score.

### Description

Computes the P-value associated with a score threshold.

### Usage

    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.

### Author(s)

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

      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)

[Package TFMPvalue version 0.0.8 Index]