knnPredict: Predict annotations of query cells from the reference using...

In symphony: Efficient and Precise Single-Cell Reference Atlas Mapping

Predict annotations of query cells from the reference using k-NN method

Description

Predict annotations of query cells from the reference using k-NN method

Usage

knnPredict(
  query_obj,
  ref_obj,
  train_labels,
  k = 5,
  save_as = "cell_type_pred_knn",
  confidence = TRUE,
  seed = 0
)

Arguments

query_obj	Symphony query object
ref_obj	Symphony reference object
train_labels	vector of labels to train
k	number of neighbors
save_as	string that result column will be named in query metadata
confidence	return k-NN confidence scores (proportion of neighbors voting for the predicted annotation)
seed	random seed (k-NN has some stochasticity in the case of ties)

Value

Symphony query object, with predicted reference labels stored in the 'save_as' slot of the query$meta_data

symphony documentation built on Jan. 17, 2023, 1:13 a.m.