resultsMatrix: DESeq aggregate results matrix

In steinbaugh/DESeqAnalysis: DESeq2 Analysis Utilities

Description

Generate an aggregate matrix of DESeqResults column values per contrast.

Usage

resultsMatrix(object, ...)

## S4 method for signature 'DESeqAnalysis'
resultsMatrix(
  object,
  value = c("log2FoldChange", "stat", "padj"),
  rowData = FALSE
)

## S4 method for signature 'DESeqAnalysisList'
resultsMatrix(
  object,
  value = c("log2FoldChange", "stat", "padj"),
  rowData = FALSE
)

Arguments

object	DESeqAnalysis.
value	character(1). Value type to return. Corresponds to supported DESeqResults column: log2FoldChange: log2 fold change. This will return shrunken LFC values if they are defined. stat: Wald test statistic. padj: BH adjusted P value.
rowData	logical(1). Include row (gene) annotations, bound to the left side of the data frame.
...	Additional arguments.

Value

• rowData = FALSE: matrix.

• rowData = TRUE: DataFrame.

Functions

• resultsMatrix,DESeqAnalysisList-method: Loop across the nested DESeqAnalysis objects and aggregate the corresponding result matrices. Note that the analysis names are automatically prefixed to the column names.

Note

Updated 2020-08-19.

Examples

data(deseq)

## DESeqAnalysis ====
x <- resultsMatrix(deseq)
head(x)

steinbaugh/DESeqAnalysis documentation built on Sept. 25, 2020, 5:21 a.m.