params: Parameters
In steinbaugh/pfgsea: Acid Genomics GSEA

params

R Documentation

Parameters

Description

Parameters

Arguments

`DESeqAnalysis`	`DESeqAnalysis`. Corresponding DESeq2 data used to perform GSEA.
`collection`	`character(1)`. Gene set collection name. Typically refers to `h` (hallmark), `c1`-`c7` collections from MSigDb. Can obtain using `collectionNames()` on `FgseaList` object.
`contrast`	`character(1)`. Contrast name.
`contrastSamples`	`logical(1)`. Only visualize the samples defined in the contrast.
`geneSetFiles`	`character`. Gene set file paths (i.e. GMT files). MSigDB files are recommended by default.
`headerLevel`	`integer(1)`. Markdown header level.
`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`).
`leadingEdge`	`logical(1)`. Visualize only the leading edge genes returned by GSEA. If `FALSE`, plot all genes in the gene set.
`n`	`integer(1)`. Number of significant processes to include. Bidirectional; will include `n` up- and down-regulated processes.
`nesThreshold`	`numeric(1)` or `NULL`. NES cutoff threshold. If left `NULL`, no cutoff will be applied.
`object`	Object.
`pathways`	`character`. Pathways.
`results`	`data.frame`/`data.table`. Unmodified `fgsea::fgsea` return.
`resultsList`	`list`. Results list.
`set`	`character(1)`. Gene set name, in a defined `collection`. For example, `"HALLMARK_ADIPOGENESIS"`.
`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.
`statsList`	`list`. Gene stats list.
`theme`	`theme`/`gg`. ggplot2 theme.
`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.
`...`	Additional arguments.