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

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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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

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  ## 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)
  

ge11232002/TFMPvalue documentation built on May 17, 2019, 12:13 a.m.