annotate.by.neighbors: Annotate by neighbors

In carmonalab/STACAS: STACAS: Sub-Type Anchoring Correction for Alignment in Seurat

Annotate by neighbors

Description

Given a partially annotated dataset, propagate labels to un-annotated cells (NA values) by similarity with annotated cells. This can be useful after integration of fully annotated datasets with other dataset that lack cell type annotation. Propagation of labels is done by K-nearest neighbors with annotated cells in a given dimensionality reduction (e.g. PCA space).

Usage

annotate.by.neighbors(
  obj,
  ref.cells = NULL,
  reduction = "pca",
  ndim = NULL,
  k = 20,
  ncores = 1,
  bg.pseudocount = 10^9,
  labels.col = "functional.cluster"
)

Arguments

obj	A Seurat object
ref.cells	Barcode of the cells to be used as reference to annotate all remaining cells. By default uses all annotated cells as reference (i.e. all cells with metadata column 'labels.col != NA').
reduction	Dimensionality reduction to be used for knn calculation
ndim	Number of dimensions to use in given reduction (by default use all dimensions)
k	Number of nearest neighbors for knn calculation
ncores	Number of cores for multi-thread execution
bg.pseudocount	Background counts for cell type frequency estimation
labels.col	Metadata column that stores cell type annotations to be propagated

Value

Returns a Seurat object with standard gene names. Genes not found in the standard list are removed. Synonyms are accepted when the conversion is not ambiguous.

Examples

# Fully annotate object, where partial annotations are stored in metadata column "celltype"
obj.full <- annotate.by.neighbors(obj.partial, labels.col="celltype")

carmonalab/STACAS documentation built on Feb. 3, 2024, 7:42 a.m.