| Version: | 0.0.9 |
| Date: | 2022-10-19 |
| Title: | Efficient and Accurate P-Value Computation for Position Weight Matrices |
| Description: | In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. <doi:10.1186/1748-7188-2-15>. |
| Author: | Ge Tan <ge_tan@live.com> |
| Maintainer: | Ge Tan <ge_tan@live.com> |
| Copyright: | 2007 LIFL-USTL-INRIA |
| Imports: | Rcpp(≥ 0.11.1) |
| Depends: | R (≥ 3.0.1) |
| Suggests: | testthat |
| LinkingTo: | Rcpp |
| License: | GPL-2 |
| URL: | https://github.com/ge11232002/TFMPvalue |
| BugReports: | https://github.com/ge11232002/TFMPvalue/issues |
| Type: | Package |
| NeedsCompilation: | yes |
| SystemRequirements: | C++11 |
| Collate: | TFMPvalue-sc2pv.R TFMPvalue-pv2sc.R TFMPvalue-lazyScore.R util.R |
| Packaged: | 2022-10-20 18:34:51 UTC; gtan |
| Repository: | CRAN |
| Date/Publication: | 2022-10-21 11:55:14 UTC |
Efficient and accurate P-value computation for Position Weight Matrices
Description
This package provides a novel algorithm that solves the P-value calculation problem given the score based on a Postion Weight Matrices (PWMs), or the reverse problem: finding the score give the desired P-value. This package is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
Details
The original code is taken from http://bioinfo.lifl.fr/TFM/TFMpvalue/TFM-Pvalue.tar.gz, retrived 26/03/2014.
The algorithm is described in Touzet, H., and Varre, J.-S. (2007). Efficient and accurate P-value computation for Position Weight Matrices. Algorithms Mol Biol 2, 15.
Author(s)
Ge Tan
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)
Compute score from P-value.
Description
Computes the score threshold associated with a P-value.
Usage
TFMpv2sc(mat, pvalue, 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". |
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". |
Value
The score is returned based on the matrix, given P-value.
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)
pvalue <- 1e-5
type <- "PFM"
score <- TFMpv2sc(pfm, pvalue, bg, type)
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)