runPipelineCombs: runPipelineCombs

In cindyfang70/clustREval: Evaluates Clustering

Description

A function that runs user-defined clustering pipelines by taking all possible combinations of user-provided pipeline hyperparameters. User-provided hyperparameters must match available options.

Usage

runPipelineCombs(
  sce,
  outputPrefix = "sce",
  doubletmethod = c("none"),
  filt = c("filt.default"),
  norm = c("norm.seurat"),
  sel = c("sel.vst"),
  selnb = 2000,
  dr = c("seurat.pca"),
  clustmethod = c("clust.seurat"),
  dims = c(10),
  resolution = c(0.1, 1)
)

Arguments

sce	SingleCellExperiment object with raw counts in counts slot.
outputPrefix	String indicating the prefix of the filepath that results should save to
doubletmethod	Character vector of doublet detection methods. Default: none
filt	Character vector of filtering methods. Default: filt.default
norm	Character vector of normalization methods Default: norm.seurat
sel	Character vector of selection methods. Default: sel.vst
selnb	Numeric vector of number of genes to select. Default: 2000
dr	Character vector of dimensionality reduction methods. Default: seurat.pca
clustmethod	Character vector of clustering methods Default: clust.seurat
dims	Numeric vector of dimensions for dimensionality reduction. Default: 10
resolution	Character vector of clustering resolutions. Default: 0.1, 1

Details

Valid filtering methods: filt.default, filt.lenient, filt.mad, filt.pca, filt.pca2, filt.stringent, none

Valid normalization methods: norm.none, norm.none.scaled, norm.scnorm, norm.scnorm.scaled, norm.scran, norm.scran.scaled, norm.sctransform, norm.scVI, norm.seurat, norm.seuratvst

Valid feature selection methods: sel.deviance, sel.expr, sel.fromField, sel.vst

Valid dimensionality reduction method: seurat.pca, serat.pca.noweight

Value

List of factors containing clustering results from each pipeline run.

Examples

# Example 1: Run with default parameters
data(embryo)
res <- clustREval::runPipelineCombs(sce=embryo, outputPrefix="embryo")
res

# Example 2: Run with user-defined parameters
## Not run: 
data(embryo)
filtMethods <- c("filt.lenient", "filt.stringent")
res <- runPipelineCombs(sce=embryo, outputPrefix="embryo", filt=filtMethods)
res

## End(Not run)

cindyfang70/clustREval documentation built on Dec. 19, 2021, 4:59 p.m.