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.

Normalize nucleotide counts.

Normalize nucleotide counts.

### 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 1.30.0 Index]