Read the feature dataset presence matrix.

Usage

get_presence_matrix(census, organism, measurement_name = "RNA")

Arguments

census: The census object from 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.

Value

A tiledbsoma::matrixZeroBasedView object with dataset join id & feature join id dimensions, filled with 1s indicating presence. The sparse matrix is accessed with zero-based indexes since the join id's may be zero.

Examples

census <- open_soma()
#> The stable Census release is currently 2023-12-15. Specify census_version = "2023-12-15" in future calls to open_soma() to ensure data consistency.
on.exit(census$close(), add = TRUE)
print(get_presence_matrix(census, "Homo sapiens")$dim())
#> Error in private$check_open_for_read_or_write(): Item must be open for read or write. s3://cellxgene-census-public-us-west-2/cell-census/2023-12-15/soma/