run_all_metrics: Running All Metrics

In scPOP: Metrics for Benchmarking scRNA-Seq Batch Correction

Description

Running All Metrics

Usage

run_all_metrics(
  reduction,
  metadata,
  batch_key,
  label1_key,
  label2_key,
  run_name = NULL,
  sil_width_prop = 1,
  sil_width_group_key = NULL,
  quietly = F
)

Arguments

reduction	A matrix of reduced dimensions
metadata	A data.frame containing information like batch, cell type, etc
batch_key	Name of column in metadata corresponding to batch
label1_key	Name of column in metadata corresponding to primary cell label, eg Cell type
label2_key	Name of column in metadata corresponding to secondary cell label, eg cluster identity
run_name	(optional) name to refer to dataset
sil_width_prop	(optional) proportion of data to use for silhouette_width
sil_width_group_key	(optional) which column in metadata to use for stratified sampling of data
quietly	(optional) if TRUE dont print anything

Value

A one row data.frame of calculated metrics

scPOP documentation built on Aug. 4, 2021, 5:06 p.m.