Seurat based mapping

Seurat based mapping

seuratMap(
  AIT.anndata,
  query.data,
  dims = 30,
  k.weight = 5,
  genes.to.use = NULL,
  cells.to.use = NULL
)

Arguments

AIT.anndata

A reference taxonomy anndata object.

query.data

A logCPM normalized matrix to be annotated.

dims

Number of principle component dimensions to use for FindTransferAnchors and TransferData (default = 30)

k.weight

k.weight parameter for TransferData Seurat function (default = 5)

genes.to.use

The set of genes to use for correlation calculation and/or Seurat integration (default is the highly_variable_genes associated with the current mode). Can be (1) a character vector of gene names, (2) a TRUE/FALSE (logical) vector of which genes to include, or (3) a column name in AIT.anndata$var corresponding to a logical vector of variable genes.

cells.to.use

The set of cells to include in Seurat integration (default is the filtered cell set associated with the current mode). Can either be a character vector of cell names or a TRUE/FALSE (logical) vector of which cells to include.

Value

Seurat mapping results as a data.frame.