scrna_pipeline {pipeComp}R Documentation

scrna_pipeline

Description

The 'PipelineDefinition' for the default scRNAseq clustering pipeline, with steps for doublet identification, filtering, normalization, feature selection, dimensionality reduction, and clustering. Alternative arguments should be character, numeric or logical vectors of length 1 (e.g. the function name for a method, the number of dimensions, etc). The default pipeline has the following steps and arguments:

Usage

scrna_pipeline(saveDimRed = FALSE, pipeClass = c("seurat", "sce"))

Arguments

saveDimRed

Logical; whether to save the dimensionality reduction for each analysis (default FALSE)

pipeClass

'sce' or 'seurat'; which object class to use throughout the pipeline. Note that the 'alternatives' functions have to be built around the chosen class. Given that, if running the 'scrna_alternatives', the class of whole pipeline is determined by the output of the filtering, only this step is affected by this option.

Value

A 'PipelineDefinition' object to be used with 'runPipeline'.

Examples

pip <- scrna_pipeline()
pip

[Package pipeComp version 1.0.0 Index]