p_thres: p_thres

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

p_thres

Description

Returns the probability threshold for the given classifier.

Usage

p_thres(classifier)

## S4 replacement method for signature 'scAnnotatR'
p_thres(classifier) <- value

Arguments

classifier	scAnnotatR object. The object is returned from the train_classifier function.
value	the new threshold

Value

Predicting probability threshold of object

scAnnotatR object with the new threshold.

Examples

data("tirosh_mel80_example")
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')
p_thres(classifier_b)

data("tirosh_mel80_example")
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_test <- test_classifier(classifier = classifier_b, 
test_obj = tirosh_mel80_example, assay = 'RNA', slot = 'counts', 
tag_slot = 'active.ident')
# assign a new threhold probability for prediction
p_thres(classifier_b) <- 0.4

grisslab/scAnnotatR documentation built on March 20, 2023, 2:42 a.m.