View source: R/NormalyzerStatistics.R
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, logTrans = FALSE) NormalyzerStatistics(experimentObj, logTrans = FALSE)
Instance of SummarizedExperiment containing matrix and design information as column data
Whether the input data should be log transformed
nds Generated NormalyzerStatistics instance
Matrix containing annotation information
Matrix containing (normalized) expression data
Filtered matrix with low-count rows removed
Data frame containing design conditions
Vector showing which entries are filtered (due to low count)
List with P-values for pairwise comparisons
List with FDR-values for pairwise comparisons
List with average expression values
List with log2 fold-change values for pairwise comparisons
Spot for saving vector of last used contrasts
Column containing last used conditions
Column containing last used batch conditions
data(example_stat_summarized_experiment) nst <- NormalyzerStatistics(example_stat_summarized_experiment)
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