IdentifyCellTypes: Calculate pathway enrichment profile

In BaderLab/Tempora: Pathway-based Trajectory Inference for Time-series Single Cell RNA-Seq Data

Description

Calculate cluster average gene expression profile and determine the pathway enrichment profile of each cluster

Usage

IdentifyCellTypes(exprMatrix, cluster_labels, cell_markers, threshold = 0.9)

Arguments

exprMatrix	A gene expression matrix, with genes in rows and cells in columns.
cluster_labels	A named vector of cluster identifier for each cell in the gene expression matrix
cell_markers	A list of possible cell types found in the dataset and their marker genes.
threshold	Threshold of GSVA score quantile. Cell types with GSVA scores in this quantile or higher compared to all other cell type scores for the same cluster would be included in cluster label. Numeric between 0-1, default to 0.9.

Value

A vector of cell types inferred from the expression of marker genes provided

BaderLab/Tempora documentation built on April 25, 2021, 2:10 p.m.