getNormalizedData: Obtain normalized count data

In TCC: TCC: Differential expression analysis for tag count data with robust normalization strategies

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, ])

TCC documentation built on Nov. 8, 2020, 8:20 p.m.