calcFactornew: Normalization factor.

In methylMnM: detect different methylation level (DMR)

Description

Amends of TMM normalization for our methond.

Usage

calcFactornew(obs, ref, m, k, logratioTrim=.3, sumTrim=0.05,
 doWeighting=TRUE, Acutoff=-1e10) 

Arguments

obs	Counts of treatment sample.
ref	Counts of control sample.
m	The number of CpG in each bin.
k	The number of MRE-CpG in each bin.
logratioTrim	amount of trim to use on log-ratios ("M" values)
sumTrim	amount of trim to use on the combined absolute levels ("A" values)
doWeighting	logical, whether to compute (asymptotic binomial precision) weights
Acutoff	cutoff on "A" values to use before trimming

Value

A real value larger than 0.

Author(s)

Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang

Examples

  d <- matrix( rpois(1000, lambda=5), nrow=200 )
  m<-rep(1,nrow=200 )
  k<-rep(1,nrow=200 )
  f <- calcFactornew(d[,2], d[,1], m, k, logratioTrim=.3, sumTrim=0.05,
 doWeighting=TRUE, Acutoff=-1e10) 

methylMnM documentation built on Nov. 8, 2020, 6:47 p.m.