PredictScTourPseudotime: PredictScTourPseudotime

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

PredictScTourPseudotime

Description

Predicts pseudotime from a trained sctour model.

Usage

PredictScTourPseudotime(
  seuratObj,
  modelFile,
  outputBasePath = tempdir(),
  outputReductionName = "sctour",
  metadataColName = "pseudotime",
  assayName = "RNA",
  cleanUpIntermediateFiles = TRUE
)

Arguments

seuratObj	The Seurat object containing the data.
modelFile	A path pointing to a trained scTour model.
outputBasePath	The directory where the embeddings and pseudotime will be written. These are deleted unless cleanUpIntermediateFiles=TRUE
outputReductionName	The assay name in which to store the results
metadataColName	The name of the meta.data column to store the resulting pseudotime
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.

Value

A Seurat Object with pseudotime from the supplied model written into its metadata.

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