R: Compute the score from P-value.

TFMLazyScore {TFMPvalue} | R Documentation

## Compute the score from P-value.

### Description

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

### Usage

    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.

### Author(s)

Ge Tan

### Examples

      ## 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)

[Package TFMPvalue version 0.0.8 Index]