migrateSeuratObject: Migrate Seurat object to JSON files of scNavigator

In ctlab/SCNPrep: Preparing Seurat object for use in scNavigator

Description

Migrate Seurat object to JSON files of scNavigator

Usage

migrateSeuratObject(
  object,
  species,
  assay = "RNA",
  slot = "counts",
  outdir = ".",
  userAnnotations = list(),
  token = NULL,
  name = "",
  description = "",
  link = "",
  public = F,
  curated = F,
  debug = F,
  markers = NULL,
  generateMarkers = F,
  generateGMTS = public && (!is.null(markers) || generateMarkers),
  maxReductionDims = 5,
  maxCellsPerIdent = 200
)

Arguments

object	Seurat object to convert
species	Species of the dataset. Supported values are: "mm", "hs", and "rn"
assay	Which assay to use to generate expression table and/or markers
slot	Which slot to use from the given assay to generate expression table and/or markers
outdir	Output folder to put the results. Will be created if doesn't exist
token	Unique token for scNavigator - if not given will be randomly generated.
name	Name of the dataset
description	Desription of the dataset
link	External link for the dataset
public	Should be dataset list on the main page in public. T/F
curated	Should be dataset list on the main page in curated T/F
debug	Enable test features for this dataset
markers	markers - data.frame or list of data.frames with generated markers
generateGMTS	if markers are not given, should we calculate DE and generate GMTS? T/F
userAnnotation	List of data.frame objects. Annotation to be added to the cells. Rownames must be the same as the barcodes

ctlab/SCNPrep documentation built on Dec. 19, 2021, 7:02 p.m.