calcFactornew {methylMnM} | R Documentation

## 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.

### 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)

[Package methylMnM version 1.25.0 Index]