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JuliASM

A julia package for allele-specific methylation (ASM) analysis.

Description

JuliASM is based on the method in [CITE], and it draws ideas from statistical physics and information theory to identify allele-specific methylation events at the haplotype level.

Getting Started

Prerequisites

  • julia v1.0.0 or greater.
  • git.

Installing

JuliASM and dependencies can be installed via the following command:

julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/jordiabante/JuliASM.jl.git"))'

Running the tests

In a julia session run

(v1.0) pkg> test JuliASM

Toy Example

The package includes a small toy example for illustrative purposes. The example consists of two alleles a1 and a2. The former has a mean-methylation level (MML) of 0.4, while that of the later is 0.6. Nevertheless, given the symmetry of the problem, both alleles have the same Shannon entropy. Thus differential analysis only identifies differences in terms of MML. The output bedGraph files can be found in out_path. To run the toy example run the following commands in a julia's REPL:

using JuliASM
dir = "/path/to/JuliASM.jl/test/"
b1 = "$(dir)/bam/example.a1.bam"
b2 = "$(dir)/bam/example.a2.bam"
fa = "$(dir)/fasta/example.fa"
vcf = "$(dir)/vcf/example.vcf"
out = "$(dir)/out/"
run_analysis(b1,b2,b1,vcf,fa,out;g_max=25,cov_ths=3,cov_b=20.0,win_exp=10,n_null=100,n_max=10)

Authors

  • Jordi Abante

License

This project is licensed under the MIT License - see the LICENSE.md file for details.

References

[CITE]