normalize {deepSNV} | R Documentation

## Normalize nucleotide counts.

### Description

This functions performs a `loess` normalization of the nucleotide. This experimental feature can be used to compare experiments from different libraries or sequencing runs that may have differing noise characteristics.

### Usage

    normalize(test, control, ...)

    ## S4 method for signature 'matrix,matrix'
    normalize(test, control, round=TRUE, ...)

    ## S4 method for signature 'deepSNV,missing'
    normalize(test, control,  ...)

### Arguments

`test` | Either an `deepSNV-class` object or a named matrix with nucleotide counts.
`control` | Missing if test is an `link{deepSNV-class}` object, otherwise a matrix with nucleotide counts.
`...` | Parameters passed to `loess`.
`round` | Logical. Should normalized counts be rounded to integers? Default=TRUE

### Value

A `deepSNV-class` object.

### Note

This feature is somewhat experimental and the results should be treated with care. Sometimes it can be better to leave the data unnormalized and use a model with greater dispersion instead.

### Author(s)

Moritz Gerstung

### Examples

    data(phiX, package = "deepSNV")
    plot(phiX)
    phiN <- normalize(phiX, round = TRUE)
    plot(phiN)

[Package deepSNV version 1.40.0 Index]