DoLdaParameterScan: DoLdaParameterScan

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

DoLdaParameterScan

Description

This will run LDA on the target assay

Usage

DoLdaParameterScan(
  seuratObj,
  ntopics = seq(5, 50, by = 5),
  normalizationMethod = "CLR",
  varFeatures = 5000,
  randomSeed = GetSeed(),
  assayName = Seurat::DefaultAssay(seuratObj),
  nCores = 1
)

Arguments

seuratObj	A Seurat object.
ntopics	Passed to runLDA.
normalizationMethod	The method used for Seurat::NormalizeData()
varFeatures	The number of variable features to use in the LDA model. The more features that are used, the slower the model will run and the more noise that will be introduced, but the model will be more complete in representing your entire dataset.
randomSeed	Passed to runLDA seed.number argument
assayName	The name of the source assay
nCores	The number of cores to use

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.