CpelAsm

Description

CpelAsm is a julia package especifically designed 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.

Installation

CpelAsm and dependencies can be installed via the following command in julia's REPL:

(v1.3) pkg> add https://github.com/jordiabante/CpelAsm.jl.git

Run the following command to load and test the CpelAsm.jl package

(v1.3) pkg> test CpelAsm

Local installation

1. Place the CpelAsm folder in a directory of your choice.

2. Start Julia and change the current directory to the CpelAsm folder on your system. To do so, type (for example):

   # Windows
   julia> cd("C:\\Users\\UserName\\code\\CpelAsm.jl")
   # macOS/Unix
   julia> cd("/Users/UserName/code/CpelAsm.jl")

3. Run the following commands to install dependencies:

   julia> using Pkg; Pkg.activate("."); Pkg.instantiate()

4. Run the following command to load and test the CpelAsm.jl package:

   julia> using CpelAsm; Pkg.test("CpelAsm")

5. If successfully installed, you should see the following prompt:

       Testing CpelAsm tests passed

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;win_exp=10,n_null=1000,cov_ths=5)

Alternatively, if the installation has been done locally, this can be simply run using the following shell command in the CpelAsm.jl folder:

julia calls/ToyExample.jl

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 11, 5238 (2020), https://doi.org/10.1038/s41467-020-19077-1.