doGSEA: Runs preranked gene set enrichment analysis.
In cailab-tamu/scTypeGSEA: Single Cell Type Gene Set Enrichment Analysis

Description Usage Arguments Value Examples

The function does gene set enrichment analysis(GSEA) for each cluster with its gene ranks. It will return cell type for each cluster.

1	doGSEA(cluster_list, db = "PanglaoDB_list", minSize = 15, maxSize = 500)

`cluster_list`	A ranked gene list for each cluster.
`db`	The cell type data base to use. For single cell data, we provide three data base, the first one is 'PanglaoDB' data base (db = 'PanglaoDB_list'), the second one is 'GSEA' data base (db = 'GSEA_list') and the third one is the reference genome for Arabidopsis (db = 'TAIR_list'). It can also be a path to the new (referential) data base that hope to be used, the file must be 'rds' format.
`minSize`	An integer value. Minimal size of a gene set to test. All pathways below the threshold are excluded.
`maxSize`	An integer value. Maximal size of a gene set to test. All pathways above the threshold are excluded.

Cell type for each cluster, and its NSF and padj.

pbmc_example <- scqc(small_pbmc_rna, min.cells = 1, min.features = 10, nfeatures = 100, npcs = 10)
          pbmc_example <- doClustering(pbmc_example, dims = 1:10, k.param = 5, resolution = 0.75)
          cluster_list <- getFC(pbmc_example, min.pct = 0.25, test.use = "MAST")
          cluster_celltype <- doGSEA(cluster_list = cluster_list, minSize = 5)