scClassifR: scClassifR class.

In grisslab/scClassifR: Pretrained learning models for cell type prediction on single cell RNA-sequencing data

Description

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

Usage

scClassifR(cell_type, clf, features, p_thres, parent)

scClassifR(cell_type, clf, features, p_thres, parent)

Arguments

cell_type	character. Name of the cell type.
clf	list. Trained model returned by caret train function.
features	vector/character containing features 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 scClassifR object.

Slots

cell_type

character. Name of the cell type.

clf

list. Trained model returned by caret train function.

features

vector/character containing features 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_features_B = c("CD19", "MS4A1", "CD79A")
set.seed(123)
clf_b <- train_classifier(train_obj = tirosh_mel80_example, 
                          features = selected_features_B, 
                          cell_type = "B cells")

clf_b

grisslab/scClassifR documentation built on Oct. 27, 2021, 12:13 p.m.