TrainSctourModel: TrainSctourModel

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

TrainSctourModel

Description

Trains an sctour model on a Seurat object

Usage

TrainSctourModel(
  seuratObj,
  modelFileName,
  featureExclusionList = "VariableGenes_Exclusion.2",
  outputBasePath = "./",
  assayName = "RNA",
  cleanUpIntermediateFiles = TRUE,
  outputReductionName = "sctour",
  metadataColName = "pseudotime"
)

Arguments

seuratObj	The Seurat object containing the data.
modelFileName	The model's file name. The full name of the model will be modelFileName.pth
featureExclusionList	A vector of gene names to be excluded from variable feature selection in model training. This supports RIRA's ExpandGeneList
outputBasePath	A directory that will store the resulting pytorch model after model training.
assayName	Assay whose data is to be written out with DropletUtils::write10xCounts. Should be "RNA".
cleanUpIntermediateFiles	This boolean controls if GEXOutfile, embeddingOutFile, and exclusionJsonPath should be deleted after model training.
outputReductionName	The assay name in which to store the results
metadataColName	The name of the meta.data column to store the resulting pseudotime

Value

A seurat object with pseudotime and dimensional reductions computed by scTour

bimberlabinternal/CellMembrane documentation built on Dec. 25, 2024, 8:10 a.m.