CreateSinglerSeuratObject: Wrapper function to create a SingleR object + Seurat object
In dviraran/SingleR: Reference-based single-cell RNA-seq annotation

Wrapper function to create a SingleR object + Seurat object

CreateSinglerSeuratObject(counts, annot = NULL, project.name,
  min.genes = 200, technology = "10X", species = "Human",
  citation = "", ref.list = list(), normalize.gene.length = F,
  variable.genes = "de", fine.tune = T, reduce.file.size = T,
  do.signatures = F, min.cells = 2, npca = 10,
  regress.out = "nUMI", do.main.types = T, reduce.seurat.object = T,
  temp.dir = NULL, numCores = SingleR.numCores)

`counts`	a tab delimited text file containing the counts matrix, a 10X directory name or a matrix with the counts.
`annot`	a tab delimited text file or a data.frame. Rownames correspond to column names in the counts data
`project.name`	the project name
`min.genes`	Include cells where at least this many genes are detected.
`technology`	The technology used for creating the single-cell data.
`species`	The species of the sample ('Human' or 'Mouse')
`citation`	a citation for the project
`ref.list`	a list of reference objects. If NULL uses the predefined reference objects - Mouse: ImmGen and Mouse.RNAseq, Human: HPCA and Blueprint+Encode.
`normalize.gene.length`	if a full-length method set to TRUE, if a 3' method set to FALSE.
`variable.genes`	variable gene method to use - 'sd' or 'de'. Default is 'de'.
`fine.tune`	perform fine tuning. Default is TRUE. Fine-tuning may take long to run.
`reduce.file.size`	remove less used SingleR fields that increase the object size.
`do.signatures`	create signatures data
`min.cells`	include genes with detected expression in at least this many cells. Will subset the raw.data matrix as well. To reintroduce excluded genes, create a new object with a lower cutoff.
`npca`	a vector of the dimensions to use in construction of the clustering and tSNE plot
`regress.out`	variables to regress out (previously latent.vars in RegressOut). For example, nUMI, or percent.mito.
`do.main.types`	run the SingleR pipeline for main cell types (cell types grouped together) as well.
`reduce.seurat.object`	if TRUE removes the raw data and other high memory objects from the Seurat object.
`temp.dir`	used by the SingleR web app.
`numCores`	Number of cores to use.