GetTransferPredictions: Get the predicted identity

In satijalab/seurat: Tools for Single Cell Genomics

Get the predicted identity

Description

Utility function to easily pull out the name of the class with the maximum prediction. This is useful if you've set prediction.assay = TRUE in TransferData and want to have a vector with the predicted class.

Usage

GetTransferPredictions(
  object,
  assay = "predictions",
  slot = "data",
  score.filter = 0.75
)

Arguments

object	Seurat object
assay	Name of the assay holding the predictions
slot	Slot of the assay in which the prediction scores are stored
score.filter	Return "Unassigned" for any cell with a score less than this value

Value

Returns a vector of predicted class names

Examples

## Not run: 
  prediction.assay <- TransferData(anchorset = anchors, refdata = reference$class)
  query[["predictions"]] <- prediction.assay
  query$predicted.id <- GetTransferPredictions(query)

## End(Not run)

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.