BenchmarkELeFHAnt: Benchmark ELeFHAnt against scPred and Label Transfer

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

Benchmark ELeFHAnt against scPred and Label Transfer

Description

Celltype annotation is a function to annotate celltypes in a single cell datasets. Benchmark ELeFHAnt is an easy to use function if the user wants to compare the predictions from ELeFHAnt to Label Transfer and scPred

Usage

BenchmarkELeFHAnt(
  reference = reference,
  query = query,
  downsample = TRUE,
  downsample_to = 1000,
  selectvarfeatures = 2000,
  ntree = 500,
  annotationCol = "Celltypes"
)

Arguments

reference	a processed Seurat Object with Celltypes column in metadata
query	a processed seurat object with seurat_clusters column in metadata
downsample	logical Indicator (TRUE or FALSE) to downsample reference, enabling fast computation.
downsample_to	a numerical value > 1 to downsample cells Default: 1000
selectvarfeatures	number of variable features to select while training (Default: 2000)
ntree	number of trees randomForest classifier should build (Default: 500)
annotationCol	Name of column in metdata which has Celltypes information in reference Default: Celltypes

Value

query seurat object with predictions from ELeFHAnt, Label Transfer and scPred added to meta.data of the object

Author(s)

Praneet Chaturvedi & Konrad Thorner

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