RunAzimuthATAC: Run Azimuth annotation for ATAC query

In satijalab/azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data

Run Azimuth annotation for ATAC query

Description

Run Azimuth annotation for ATAC query

Usage

## S3 method for class 'Seurat'
RunAzimuthATAC(
  query,
  reference,
  fragment.path = NULL,
  annotation.levels = NULL,
  umap.name = "ref.umap",
  verbose = TRUE,
  assay = NULL,
  k.weight = 50,
  n.trees = 20,
  mapping.score.k = 100,
  dims.atac = 2:50,
  dims.rna = 1:50
)

## S3 method for class 'character'
RunAzimuthATAC(query, ...)

RunAzimuthATAC(query, ...)

Arguments

query	Seurat object or following type of path: A .h5 matrix A .rds file containing a Seurat object A .h5ad anndata object A .h5seurat object
reference	Name of reference to map to or a path to a directory containing ext.Rds
annotation.levels	list of annotation levels to map. If not specified, all will be mapped.
umap.name	name of umap reduction in the returned object
assay	query assay name
dims.atac	dimensions
dims.rna	dimensions
do.adt	transfer ADT assay

Value

Seurat object with reference reductions and annotations

Returns a Seurat object containing celltype annotations

satijalab/azimuth documentation built on Nov. 19, 2023, 8:34 a.m.