NormalyzerStatistics {NormalyzerDE} | R Documentation

## Class representing a dataset for statistical processing in NormalyzerDE

### Description

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.

### Usage

    NormalyzerStatistics(experimentObj, logTrans = FALSE)

    NormalyzerStatistics(experimentObj, logTrans = FALSE)

### Arguments

`experimentObj` | Instance of SummarizedExperiment containing matrix and design information as column data
`logTrans` | Whether the input data should be log transformed

### Value

nds Generated NormalyzerStatistics instance

### Slots

`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

`contrasts`

  Spot for saving vector of last used contrasts

`condCol`

  Column containing last used conditions

`batchCol`

  Column containing last used batch conditions

### Examples

    data(example_stat_summarized_experiment)
    nst <- NormalyzerStatistics(example_stat_summarized_experiment)

[Package NormalyzerDE version 1.4.0 Index]