https://github.com/kchu25/motifpvalue.jl

Threshold and p-value computations for Position Weight Matrices
https://github.com/kchu25/motifpvalue.jl

bioinformatics genomics julia motif motifs p-value position-weight-matrix pwm regulatory-genomics transcription-factor-binding

Last synced: 8 months ago
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Threshold and p-value computations for Position Weight Matrices

• Host: GitHub
• URL: https://github.com/kchu25/motifpvalue.jl
• Owner: kchu25
• License: mit
• Created: 2021-12-07T20:07:45.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2021-12-15T04:22:45.000Z (over 4 years ago)
• Last Synced: 2025-10-06T12:01:20.461Z (8 months ago)
• Topics: bioinformatics, genomics, julia, motif, motifs, p-value, position-weight-matrix, pwm, regulatory-genomics, transcription-factor-binding
• Language: Julia
• Homepage:
• Size: 111 KB
• Stars: 3
• Watchers: 1
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# MotifPvalue

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://kchu25.github.io/MotifPvalue.jl/dev)

[![Build Status](https://github.com/kchu25/MotifPvalue.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/kchu25/MotifPvalue.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Coverage](https://codecov.io/gh/kchu25/MotifPvalue.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/kchu25/MotifPvalue.jl)

# Introduction

This package provides two useful subroutines:

*  Given a score threshold `α`, `score2pvalue` calculates the p-value, i.e. the probability of a set of strings generated from a specfied background model such that each string in this set can attain a score higher than or equal to `α` with respect to the input `pwm`.

* Given a p-value `pval`, `pval2score` calculates the highest score `α` such that `score2pvalue(pwm,α)` is larger than or equal to `pval`.

By default, the background model is specified as i.i.d discrete uniform.

This is an implementation of:

Efficient and accurate P-value computation for Position Weight Matrices by Touzet et al.

https://almob.biomedcentral.com/articles/10.1186/1748-7188-2-15

# Basic examples

    using MotifPvalue

    # An example PWM

    pwm = [-2.86995   1.3814    1.36906  -4.88479   -4.19164  -4.88479   1.36607  -5.57793   -0.336375    1.38238;

            1.36707  -5.57793  -2.86995  -0.294869  -4.88479   1.34492  -3.49849   1.26497   -2.1768     -4.88479;

           -5.57793  -4.47899  -5.57793   1.11923   -3.78584  -5.57793  -4.88479  -5.57793    0.798703   -5.57793;

           -4.19164  -5.57793  -4.88479  -1.68576    1.375    -1.88885  -3.17976  -0.798616  -0.0526305  -5.57793];

    

    # Compute pvalue with pwm and score = 4

    score2pvalue(pwm, 4)

    > 0.000213623046875

    # Compute the score-threshold for p-value 1e-4

    pvalue2score(pwm, 1e-4)

    > 5.57