labelCelltype: Add cell type to Seurat object.

In cailab-tamu/scTypeGSEA: Single Cell Type Gene Set Enrichment Analysis

Description

Add cell type to Seurat object.

Usage

labelCelltype(obj, cluster_celltype)

Arguments

obj	A Seurat object with cluster.
cluster_celltype	A matrix. Each row is one cell type, contains NSF and padj.

Value

It will return a list including a Seurat object with cell type for each cell and a cell type matrix.

Examples

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)
          celltype <- labelCelltype(pbmc_example, cluster_celltype)

cailab-tamu/scTypeGSEA documentation built on July 15, 2020, 10:56 a.m.