TFMPvalue-lazyScore: Compute the score from P-value.

In TFMPvalue: Efficient and Accurate P-Value Computation for Position Weight Matrices

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)
  

TFMPvalue documentation built on Oct. 21, 2022, 5:06 p.m.