methylMnM (version 1.10.0)

calcFactornew: Normalization factor.

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.

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)