NormalyzerStatistics {NormalyzerDE} | R Documentation |
Is initialized with an annotation matrix, a data matrix and a design data frame. This object can subsequently be processed to generate statistical values and in turn used to write a full matrix with additional statistical information as well as a graphical report of the comparisons.
NormalyzerStatistics(experimentObj, conditionCol = "group", logTrans = FALSE, leastRepCount = 2) NormalyzerStatistics(experimentObj, conditionCol = "group", logTrans = FALSE, leastRepCount = 2)
experimentObj |
Instance of SummarizedExperiment containing matrix and design information as column data |
conditionCol |
Column in column data containing the condition information for which contrasts will be performed |
logTrans |
Whether the input data should be log transformed |
leastRepCount |
Least replicates in each group to be retained for contrast calculations |
nds Generated NormalyzerStatistics instance
annotMat
Matrix containing annotation information
dataMat
Matrix containing (normalized) expression data
filteredDataMat
Filtered matrix with low-count rows removed
designDf
Data frame containing design conditions
filteringContrast
Vector showing which entries are filtered (due to low count)
pairwiseCompsP
List with P-values for pairwise comparisons
pairwiseCompsFdr
List with FDR-values for pairwise comparisons
pairwiseCompsAve
List with average expression values
pairwiseCompsFold
List with log2 fold-change values for pairwise comparisons
data(example_stat_summarized_experiment) nst <- NormalyzerStatistics(example_stat_summarized_experiment)