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, conditionCol = "group",
  logTrans = FALSE, leastRepCount = 2)

NormalyzerStatistics(experimentObj, conditionCol = "group",
  logTrans = FALSE, leastRepCount = 2)

Arguments

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

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

Examples

data(example_stat_summarized_experiment)
nst <- NormalyzerStatistics(example_stat_summarized_experiment)

[Package NormalyzerDE version 1.0.0 Index]