getNormalizedData {TCC} | R Documentation |
This function generates normalized count data from both original count data and calculated normalization factors.
getNormalizedData(tcc)
tcc |
TCC-class object. |
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.
A numeric matrix containing normalized count data.
# 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, ])