imputeKNN: Impute the query cell expression matrix

In rliger: Linked Inference of Genomic Experimental Relationships

Impute the query cell expression matrix

Description

Impute query features from a reference dataset using KNN.

Usage

imputeKNN(
  object,
  reference,
  queries,
  knn_k = 20,
  weight = TRUE,
  norm = TRUE,
  scale = FALSE,
  verbose = TRUE
)

Arguments

object	liger object.
reference	Dataset containing values to impute into query dataset(s).
queries	Dataset to be augmented by imputation. If not specified, will pass in all datasets.
knn_k	The maximum number of nearest neighbors to search. (default 20)
weight	Whether to use KNN distances as weight matrix (default FALSE).
norm	Whether normalize the imputed data with default parameters (default TRUE).
scale	Whether scale but not center the imputed data with default parameters (default TRUE).
verbose	Print progress bar/messages (TRUE by default)

Value

liger object with raw data in raw.data slot replaced by imputed data (genes by cells)

Examples

## Not run: 
# Only runable for ATAC dataset. See tutorial on GitHub.
# ligerex (liger object), factorization complete
# impute every dataset other than the reference dataset
ligerex <- imputeKNN(ligerex, reference = "y_set", weight = FALSE)
# impute only z_set dataset
ligerex <- imputeKNN(ligerex, reference = "y_set", queries = list("z_set"), knn_k = 50)

## End(Not run)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.