epiG.algorithm.config: Create a epiG configuration

In epiG: DNA methylation and SNP calling for bisulfite sequencing data

Description

Create a epiG configuration

Usage

  epiG.algorithm.config(ref.file, alt.file,
    max_iterations = 1e+05,
    prior = list(create_genotype_prior_ref(), create_genotype_prior_alt()),
    model = create_bisulfite_model(),
    sequence_quality_adjust = 0.1, haplo_prior = 0.2,
    ref_prior = 0.9, min_overlap_length = 1,
    chunk_size = 1000, chunk_method = "reads",
    reads_hard_limit = 1500, verbose = TRUE)

Arguments

ref.file
alt.file
max_iterations
prior
model
sequence_quality_adjust
haplo_prior	modeled using a geometric distribution
ref_prior
min_overlap_length
chunk_size
chunk_method
reads_hard_limit
verbose

Value

epiG configuration

Author(s)

martin

epiG documentation built on May 2, 2019, 6:49 p.m.