scGate (version 1.7.0)

test_my_model: Test your model

Description

Wrapper for fast model testing on 3 sampled datasets

Usage

test_my_model(
  model,
  testing.version = "hsa.latest",
  custom.dataset = NULL,
  target = NULL,
  plot = TRUE
)

Value

Returns performance metrics for the benchmarking datasets, and optionally plots of the predicted cell type labels in reduced dimensionality space.

Arguments

model

scGate model in data.frame format

testing.version

Character indicating the version of testing tatasets to be used. By default "hsa-latest" will be used. It will be ignored if a custom dataset is provided (in Seurat format).

custom.dataset

Seurat object to be used as a testing dataset. For testing purposes, metadata seurat object must contain a column named 'cell_type' to be used as a gold standard. Also a set of positive targets must be provided in the target variable.

target

Positive target cell types. If default testing version is used this variable must be a character indicating one of the available target models ('immune','Lymphoid','Myeloid','Tcell','Bcell','CD8T','CD4T', 'NK','MoMacDC','Plasma_cell','PanBcell'). If a custom dataset is provided in Seurat format, this variable must be a vector of positive cell types in your data. The last case also require that such labels were named as in your cell_type meta.data column.

plot

Whether to return plots to device

Examples

# \donttest{
scGate.model.db <- get_scGateDB()
# Browse the list of models and select one:
model.panBcell <-  scGate.model.db$human$generic$PanBcell
# Test the model with available testing datasets
panBcell.performance <- test_my_model(model.panBcell, target = "PanBcell")
model.Myeloid <-  scGate.model.db$human$generic$Myeloid
myeloid.performance <- test_my_model(model.Myeloid, target = "Myeloid")
# }