Generate an aggregate matrix of DESeqResults column values per contrast.

resultsMatrix(object, ...)

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

# S4 method for 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 2021-03-15.

Examples

data(deseq) ## DESeqAnalysis ==== x <- resultsMatrix(deseq) head(x)
#> condition_B_vs_A treatment_D_vs_C #> gene001 0.68113957 1.348785e-02 #> gene002 0.21751307 -6.657954e-03 #> gene003 0.16882225 2.948482e-05 #> gene004 0.02745442 1.209473e-02 #> gene005 -0.23444214 -1.047561e-02 #> gene006 -0.56577498 7.519695e-03