TFMsc2pv {TFMPvalue}

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)