data_SAFE: An expression_matrix.csv (32738 genes and 500 cells of three...

In yycunc/SAFEclustering: SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

Description

An expression_matrix.csv (32738 genes and 500 cells of three cell types, cd56_NK cells, b cells and regulatory T cells from 10X Genomices (Zheng et al. 2016)), and celltype.info.csv (List of cell type and cluster information for the 500 cells).

Usage

data("data_SAFE")

Format

An object of class list of length 4.

Examples

# Load the example data data_SAFE
data("data_SAFE")
working.dir = "~/Documents/single_cell_clustering"

# Zheng dataset
# Run individual_clustering
cluster.result <- individual_clustering(inputTags=data_SAFE$Zheng.expr, SEED=123)

# Cluster ensemble using SAFE clustering:
cluster.ensemble <- SAFE(cluster_results=cluster.result, program.dir = working.dir, SEED=123)

# Biase dataset
# Run individual_clustering
cluster.result <- individual_clustering(inputTags = data_SAFE$Biase.expr, datatype = "FPKM", seurat_min_cell = 200, resolution_min = 1.2, tsne_min_cells = 200, tsne_min_perplexity = 10, SEED=123)

# Cluster ensemble using SAFE clustering:
cluster.ensemble <- SAFE(cluster_results=cluster.result, program.dir = working.dir, SEED=123)

yycunc/SAFEclustering documentation built on March 29, 2021, 5:58 a.m.