CpelAsm

Toy Example

The package includes a small toy example, which should take no more than 20 seconds to run, for illustrative purposes. The example in particular consists of 2 haplotypes in a single chromosome of an artificial reference genome. Each haplotype has two alleles: a1 and a2. For simplicity, CpG sites in both alleles are distributed independently according to a Bernoulli distribution. In a1, the probability of methylation is p1=0.8, while in a2 the probability of methylation is p2=0.2. Thus, CpG sites in the former have a mean methylation level (MML) of 0.8, while that of the later is 0.2. Given the symmetry of the problem, however, both alleles have the same Shannon entropy (see Shannon entropy of a flip coin). Thus differential analysis only identifies ASM imbalances in for statistics Tmml and Tpdm. That is, CpelAsm only identifies mean methylation level differences and probability distribution of methylation differences. The output bedGraph files with the suffix pvals contain the results of the statistical test performed for each haplotype. These files can be found in the out/ directory. To run the toy example run the following commands in a julia's REPL:

# Load CpelAsm
using CpelAsm

# Define I/O
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 CpelAsm
run_analysis(b1,b2,b1,vcf,fa,out;g_max=50,win_exp=10,n_null=50,n_max=10)