computeClusterEvalStats: Calculate statistics for evaluating batch correction

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

Calculate statistics for evaluating batch correction

Description

Calculate statistics for evaluating batch correction

Usage

computeClusterEvalStats(
  spe_object,
  foiColumn,
  precomputed = NULL,
  n_dimension = c(1, 2),
  assay = 2
)

Arguments

spe_object	A Spatial Experiment object.
foiColumn	A column name indicating the factor of interest to be tested, can be biological factor or batch factor.
precomputed	a dimensional reduction results from stats::prcomp. result in reducedDims(object) to plot. Default is NULL, we will compute for you.
n_dimension	The top n dimensions to be plotted
assay	a numeric or character, specifying the assay to use (for SummarizedExperiment and its derivative classes).

Value

A dataframe object containing the clustering evaluating statistics.

Examples

library(scater)
data("dkd_spe_subset")
computeClusterEvalStats(dkd_spe_subset, "SlideName")

DavisLaboratory/standR documentation built on March 28, 2024, 4:23 a.m.