PostAdjustment: Post Adjustment

Description Usage Arguments Value

View source: R/PostAdjustment.R

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

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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.