resultsMatrix: DESeq aggregate results matrix

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

DESeq aggregate results matrix

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", "alpha"),
  rowData = FALSE
)

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

Arguments

object	Object.
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. alpha: Either (1) padj, the BH adjusted P value; or (2) svalue, the s-value, when using apeglm (or ashr).
rowData	logical(1). Include row (gene) annotations, bound to the left side of the data frame.
...	Additional arguments.

Value

• rowData = FALSE: matrix.

• rowData = TRUE: DFrame.

Functions

• resultsMatrix(DESeqAnalysisList): 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 2022-05-17.

Examples

data(deseq)

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

steinbaugh/DESeqAnalysis documentation built on Oct. 13, 2023, 5:39 a.m.