Skip to content

Latest commit

 

History

History
72 lines (52 loc) · 2.2 KB

README.md

File metadata and controls

72 lines (52 loc) · 2.2 KB
Raw

CpelAsm

CI Docs MIT license

Description

CpelAsm is a julia package especifically desgined for haplotype allele-specific methylation based on the method in [1]. CpelAsm draws ideas from statistical physics and information theory to detect allele-specific methylation imbalances at the haplotype level.

Testing

CpelAsm is tested against Julia 1.3.0 on the latest versions of Linux, macOS and Windows.

Getting Started

Prerequisites

  • julia v1.3.0
  • git.

Installing

CpelAsm and dependencies can be installed via the following command:

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

Running the tests

In a julia session run

(v1.3) pkg> test CpelAsm

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 0.8, while that of the later is 0.2. 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 CpelAsm
dir = "/path/to/CpelAsm.jl/test/"
b1 = "$(dir)/bam/example.a1.bam"
b2 = "$(dir)/bam/example.a2.bam"
fa = "$(dir)/fasta/n-masked/example.fa"
vcf = "$(dir)/vcf/example.vcf"
out = "$(dir)/out/"
run_analysis(b1,b2,b1,vcf,fa,out;g_max=50,cov_ths=5,cov_b=2.0,win_exp=10,n_null=50,n_max=10)

Authors

  • Jordi Abante

License

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

References

[1] Abante, J., Fang, Y., Feinberg, A.P., Goutsias, J., Detection of haplotype-dependent allele-specific DNA methylation in WGBS data, Nature Communications 2020 XYZ.