Convenience wrapper around SOMAExperimentAxisQuery, to build and execute a query, and return it as a Seurat object.

Convenience wrapper around SOMAExperimentAxisQuery, to build and execute a query, and return it as a Seurat object.

Usage

get_seurat(
  census,
  organism,
  measurement_name = "RNA",
  X_name = "raw",
  obs_query = NULL,
  obs_column_names = NULL,
  var_query = NULL,
  var_column_names = NULL
)

Arguments

census

The census object, usually returned by cellxgene.census::open_soma().

organism

The organism to query, usually one of Homo sapiens or Mus musculus

measurement_name

The measurement object to query. Defaults to RNA.

X_name

The X layer to query. Defaults to raw.

obs_query

A SOMAAxisQuery for the obs axis.

obs_column_names

Columns to fetch for the obs data frame.

var_query

A SOMAAxisQuery for the var axis.

var_column_names

Columns to fetch for the var data frame.

Value

A Seurat object containing the sensus slice.