benchmarkCluster: Examine cluster-specific scoring performance for...

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Examine cluster-specific scoring performance for cluster-specific gene sets that have been variably contaminated with random genes.

Description

Examine cluster-specific scoring performance for cluster-specific gene sets that have been variably contaminated with random genes.

Usage

benchmarkCluster(
  object,
  benchmark_data,
  benchmark_genesets,
  which_cluster,
  miko.fdr.threshold = 0.05,
  coherence.fraction.threshold = 0
)

Arguments

object	Seurat Object
benchmark_data	'benchmark_data' returned in list from 'benchmarkScores' function. Must run 'benchmarkScores' prior to 'benchmarkCluster'.
benchmark_genesets	'benchmark_genesets' returned in list from 'benchmarkScores' function. Must run 'benchmarkScores' prior to 'benchmarkCluster'.
miko.fdr.threshold	FDR threshold for Miko scores. Default is 0.05.
coherence.fraction.threshold	Coherence fraction threshold. Default is 0.8.
which.cluster	Name of group within grouping variable used to run ‘benchmarkScores'. E.g., ’3' if 'benchmarkScores(... , group_by = "seurat_clusters")'

Value

list of benchmark results for specified cluster.

Author(s)

Nicholas Mikolajewicz

See Also

benchmarkScores for miko scoring benchmarking

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.