Class containing parameterized ranked gene lists.

Return a parameterized ranked list for each differential expression contrast.

RankedList(object, ...)

# S4 method for matrix
RankedList(object, value = "log2FoldChange")

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

# S4 method for FGSEAList
RankedList(object)

Arguments

object

Object.

...

Additional arguments.

value

character(1). Value type to use for GSEA. Currently supported:

  1. stat: Wald test statistic. This column is returned by results() but is removed in DESeq2::lfcShrink() return, currently.

  2. log2FoldChange: Shrunken log2 fold change. Note that this option requires DESeq2::lfcShrink() return to be slotted.

  3. padj: Adjusted P value. This don't provide directional ranks, but is offered as a legacy option. Not generally recommended.

Value

RankedList.

Gene symbol multi-mapping

Multiple gene IDs can map to a gene symbol (e.g. Homo sapiens HGNC names). In this event, we're averaging the stat values using mean() internally.

Examples

data(deseq, package = "DESeqAnalysis") x <- RankedList(deseq) print(x)
#> RankedList of length 1 #> names(1): condition_B_vs_A