PostAdjustment: Post Adjustment

In Tieming/A-Bayesian-hidden-Markov-model-for-detecting-DMRs: DMR detection by HMM

Description

This function adjusts HMM output such that each detected DMR has a minimum length and a minimum number of CpGs in each DMR.

Usage

PostAdjustment(em.o, CpG.pos, min.length = 500, min.CpGs = 3,
  max.gap = 300)

Arguments

em.o	Output from EM function.
CpG.pos	Contains all CpG positions.
min.length	Minimum length of a DMR. Default to 500.
min.CpGs	Minimum number of CpGs contained in a DMR. Default to 3.
max.gap	Maximum gap between any two CpGs. Default to 300.

Value

dmr.res A matrix contains transformed observations for each bin and the adjusted predictions for each bin (0-normal, 1-hyper, 2-hypo).

region A matrix contains detected regions satisfying user-defined length and number of CpGs.

Tieming/A-Bayesian-hidden-Markov-model-for-detecting-DMRs documentation built on May 29, 2019, 12:36 p.m.