scAnnotatR {scAnnotatR} | R Documentation

## scAnnotatR class.

### Description

This class is returned by the `train_classifier` function. Generally, scAnnotatR objects are never created directly.

### Usage

    scAnnotatR(cell_type, caret_model, marker_genes, p_thres, parent)

    scAnnotatR(cell_type, caret_model, marker_genes, p_thres, parent)

### Arguments

`cell_type` | character. Name of the cell type.
`caret_model` | list. Trained model returned by caret train function.
`marker_genes` | vector/character containing marker genes used for the training.
`p_thres` | numeric. Probability threshold for the cell type to be assigned for a cell.
`parent` | character. Parent cell type.

### Value

A scAnnotatR object.

### Slots

`cell_type`

  character. Name of the cell type.

`caret_model`

  list. Trained model returned by caret train function.

`marker_genes`

  vector/character containing marker genes used for the training.

`p_thres`

  numeric. Probability threshold for the cell type to be assigned for a cell.

`parent`

  character. Parent cell type.

### Examples

    # load small example dataset
    data("tirosh_mel80_example")

    # train a classifier, for ex: B cell
    selected_marker_genes_B = c("CD19", "MS4A1", "CD79A")
    set.seed(123)
    classifier_b <- train_classifier(train_obj = tirosh_mel80_example,
    assay = 'RNA', slot = 'counts', marker_genes = selected_marker_genes_B,
    cell_type = "B cells", tag_slot = 'active.ident')

    classifier_b

[Package scAnnotatR version 1.0.0 Index]