normalizeTomo {tomoda} | R Documentation

## Normalize data

### Description

Normalize the raw read count in a `SummarizedExperiment` object.

### Usage

    normalizeTomo(object, method = "median")

### Arguments

`object` | A `SummarizedExperiment` object.
`method` | Character, must be one of `"median"`, or `"cpm"`.

### Details

This function should be run for `SummarizedExperiment` object created from raw read count matrix. If the `SummarizedExperiment` object already has a normalized count matrix. The function simply return the original object. Library sizes of all sections are normalized to the median library size (method='median') or one million (method='cpm').

### Value

A `SummarizedExperiment` object with normalized read count matrix saved in assay `'normalized'`.

### Examples

    data(zh.data)
    zh <- createTomo(zh.data, normalize=FALSE)
    zh <- normalizeTomo(zh)

[Package tomoda version 1.0.0 Index]