meth_state_finder: Infer Differential Methylation Status

In cgplab/ROCkerMeth: Receiver Operating Characteristic curves analyzer for DNA methylation data

Infer Differential Methylation Status

Description

This function classifies CpG sites as hypo-methylated (1), non-differentially methylated (2) or hyper-methylated (3) using a Heterogeneous Hidden Markov Model (HMM).

Usage

meth_state_finder(
  input_signal,
  input_pos,
  auc_sd,
  pt_start,
  normdist,
  ratiosd,
  mu,
  use_trunc
)

Arguments

input_signal	A numeric vector of AUC scores.
input_pos	An integer vector of chromosomal locations
auc_sd	Standard deviation of AUC signal (genome wide).
pt_start	Transition probability of the HSLM.
normdist	Distance normalization parameter of the HSLM.
ratiosd	Fraction between the standard deviation of AUC values of differentially methylated sites and the total standard deviation of AUC values.
mu	Expected mean (AUC) for hypo-methylated state (1-mu is the expected mean for hyper-methylated state).
use_trunc	Use truncated normal distribution (DEBUGGING ONLY).

Value

An integer vector of methylation states (1,2,3).

cgplab/ROCkerMeth documentation built on March 27, 2022, 9:57 p.m.