RankedList: Ranked list of genes

In steinbaugh/pfgsea: Acid Genomics GSEA

Ranked list of genes

Description

Class containing parameterized ranked gene lists.

Usage

RankedList(object, ...)

## S4 method for signature 'DESeqAnalysis'
RankedList(
  object,
  keyType = c("geneName", "ensemblGeneId", "ncbiGeneId"),
  value = c("stat", "log2FoldChange"),
  proteinCodingOnly = FALSE
)

## S4 method for signature 'DESeqResults'
RankedList(
  object,
  rowRanges,
  keyType = c("geneName", "ensemblGeneId", "ncbiGeneId"),
  value = c("stat", "log2FoldChange"),
  proteinCodingOnly = FALSE
)

## S4 method for signature 'FgseaList'
RankedList(object)

Arguments

object	Object.
...	Additional arguments.
keyType	'character(1). Gene identifier format: "geneName": Gene names (a.k.a. symbols; e.g. "TP53"). ⁠"ensemblGeneId⁠: Ensembl gene identifiers (e.g. "ENSG00000000003"). "ncbiGeneId": NCBI (Entrez) gene identifiers (e.g. 7157).
value	character(1). Value type to use for GSEA ranked list. Currently supported: stat: Wald test statistic. This column is returned by results() but is removed in DESeq2::lfcShrink() return, currently. log2FoldChange: Shrunken log2 fold change. Note that this option requires DESeq2::lfcShrink() return to be slotted. padj: Adjusted P value. This don't provide directional ranks, but is offered as a legacy option. Not generally recommended.
proteinCodingOnly	logical(1). Restrict to protein coding genes only.
rowRanges	GenomicRanges or GenomicRangesList. Genomic ranges (e.g. genome annotations). Metadata describing the assay rows.

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 values using mean() internally.

Note

Updated 2023-03-01.

Examples

data(deseq, package = "DESeqAnalysis")
data(fgsea)

## DESeqAnalysis ====
object <- deseq
rl <- RankedList(object)
print(rl)

## FgseaList ====
object <- fgsea
rl <- RankedList(object)
print(rl)

steinbaugh/pfgsea documentation built on Oct. 17, 2023, 11:24 a.m.