pfgsea: Acid Genomics GSEA

#' Parameters
#'
#' @name params
#' @keywords internal
#'
#' @param DESeqAnalysis `DESeqAnalysis`.
#' Corresponding DESeq2 data used to perform GSEA.
#'
#' @param collection `character(1)`.
#' Gene set collection name.
#' Typically refers to `h` (hallmark), `c1`-`c7` collections from MSigDb.
#' Can obtain using `collectionNames()` on `FgseaList` object.
#'
#' @param contrast `character(1)`.
#' Contrast name.
#'
#' @param contrastSamples `logical(1)`.
#' Only visualize the samples defined in the contrast.
#'
#' @param geneSetFiles `character`.
#' Gene set file paths (i.e. GMT files).
#' MSigDB files are recommended by default.
#'
#' @param headerLevel `integer(1)`.
#' Markdown header level.
#'
#' @param 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`).
#'
#' @param leadingEdge `logical(1)`.
#' Visualize only the leading edge genes returned by GSEA.
#' If `FALSE`, plot all genes in the gene set.
#'
#' @param n `integer(1)`.
#' Number of significant processes to include.
#' Bidirectional; will include `n` up- and down-regulated processes.
#'
#' @param nesThreshold `numeric(1)` or `NULL`.
#' NES cutoff threshold.
#' If left `NULL`, no cutoff will be applied.
#'
#' @param object Object.
#'
#' @param pathways `character`.
#' Pathways.
#'
#' @param results `data.frame`/`data.table`.
#' Unmodified `fgsea::fgsea` return.
#'
#' @param resultsList `list`.
#' Results list.
#'
#' @param set `character(1)`.
#' Gene set name, in a defined `collection`.
#' For example, `"HALLMARK_ADIPOGENESIS"`.
#'
#' @param stats `numeric`.
#' Gene stats. Test statistic is recommended by default, but shrunken log2
#' fold changes are also acceptable. Don't input unshrunken LFC values without
#' standard error correction.
#' @param statsList `list`.
#' Gene stats list.
#'
#' @param statsList `list`.
#' Gene stats list.
#'
#' @param theme `theme`/`gg`.
#' ggplot2 theme.
#'
#' @param value `character(1)`.
#' Value type to use for GSEA ranked list.
#'
#' 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.
#'
#' @param ... Additional arguments.
NULL