Description Usage Arguments Details Value Examples

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

1 | ```
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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
# 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, ])
``` |

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