Package index
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ExpressionResultSet-class - An S4 class to store differential expression results
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consensus() - Get consensus results
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consensusList() - consensusList: make a list of genes considered DE by at least 'threshold' tools
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consexpressionR-packageconsexpressionR - consexpressionR: Differential Expression Analysis using consensus of multiple methods
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createExpressionResultSet() - Constructor for ExpressionResultSet
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createNameFileOutput() - Build a file output name
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expressionDefinition() - Identify DE genes by method-specific thresholds
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frameAllGenes() - frameAllGenes
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listDeByTool() - listDeByTool: creates a data.frame with genes (rows) and DE tools (columns). Each tool that identifies a gene as DE is marked with 1.
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methodNames() - Get method names used in the analysis
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parameters() - Get parameters used in the analysis
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readCountFile() - Read table count File and creates a matrix from the given content file.
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results() - Get result tables
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runBayseq() - Run differential expression analysis using baySeq
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runDeseq2() - Execute DESeq2 DGE default analysis is configured to read only kallisto files, and count data
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runEbseq() - Execute EBSeq gene Expression analysis
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runEdger() - Execute edgeR expression Analisys
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runExpression() - Make expression analysis of multiple tools and return results by tool.
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runLimma() - Execute edgeR expression Analisys
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runNoiSeq() - Execute NOISeq gene Expression analysis
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runSamSeq() - Execute SAMSeq gene Expression analysis to count data
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show(<ExpressionResultSet>) - Show an ExpressionResultSet object
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summary(<ExpressionResultSet>) - Summarize an ExpressionResultSet object
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upSetPlotTools() - UpSet Plot shows intersections by DE indications
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writeResults() - Write a table or data.frame in defined output file