ValidatePredictions: ELeFHAnt Validate Predictions

In praneet1988/ELeFHAnt: Ensemble Learning for Harmonization and Annotation of Single Cells

ELeFHAnt Validate Predictions

Description

Validate Predictions is a function to validate celltype assignments. It uses Gene Set Enrichment Analysis (GSEA) and cell type markers from CellMarker Database to let user assess celltype annotation/harmonization. It requires species, tissue and query dataset. For GSEA, ELeFHAnt uses C8 Hallmark Gene Sets and from CellMarker Database it uses markers curated based on experiments.

Usage

ValidatePredictions(species = NULL, tissue = NULL, query = NULL)

Arguments

species	human or mouse to select the C8 hallmark cell type gene sets
tissue	please check human_tissues or mouse_tissues if validatePredictions = TRUE
query	a processed seurat object with seurat_clusters column in metadata
reference	a processed seurat object with Celltypes column in metadata

Value

GSEA result

Author(s)

Praneet Chaturvedi & Konrad Thorner

praneet1988/ELeFHAnt documentation built on July 20, 2022, 7:29 p.m.