TFMPvalue (version 0.0.4)

TFMLazyScore: 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.

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)
  pvalue <- 1e-5
  type <- "PFM"
  granularity <- 1e-5
  TFMLazyScore(pfm, pvalue, bg, type, granularity)