getNormalizedData {TCC} | R Documentation

## Obtain normalized count data

### Description

This function generates normalized count data from both original count data and calculated normalization factors.

### Usage

    getNormalizedData(tcc)

### Arguments

`tcc` | TCC-class object.

### Details

This function is generally used after the `calcNormFactors` function that calculates normalization factors. The normalized data is calculated using both the original count data stored in the `count` field and the normalization factors stored in the `norm.factors` field in the TCC-class object.

### Value

A numeric matrix containing normalized count data.

### Examples

    # Note that the hypoData has non-DEGs at 201-1000th rows.
    nonDEG <- 201:1000
    data(hypoData)
    summary(hypoData[nonDEG, ])
    group <- c(1, 1, 1, 2, 2, 2)

    # Obtaining normalized count data after performing the
    # DEGES/edgeR normalization method, i.e., DEGES/edgeR-normalized data.
    tcc <- new("TCC", hypoData, group)
    tcc <- calcNormFactors(tcc, norm.method = "tmm", test.method = "edger",
                           iteration = 1, FDR = 0.1, floorPDEG = 0.05)
    normalized.count <- getNormalizedData(tcc)
    summary(normalized.count[nonDEG, ])

    # Obtaining normalized count data after performing the TMM normalization
    # method (Robinson and Oshlack, 2010), i.e., TMM-normalized data.
    tcc <- new("TCC", hypoData, group)
    tcc <- calcNormFactors(tcc, norm.method = "tmm", iteration = 0)
    normalized.count <- getNormalizedData(tcc)
    summary(normalized.count[nonDEG, ])

[Package TCC version 1.30.0 Index]