Building the signature matrix — build

The single_cell_object is expected to have rownames() and colnames()

build_model(
  single_cell_object,
  cell_type_annotations = NULL,
  method = deconvolution_methods,
  batch_ids = NULL,
  bulk_gene_expression = NULL,
  verbose = FALSE,
  cell_type_column_name = NULL,
  markers = NULL,
  assay_name = NULL,
  ...
)

Arguments

single_cell_object: A matrix or dataframe with the single-cell data. Rows are genes, columns are samples. Row and column names need to be set. Alternatively a SingleCellExperiment or an AnnData object can be provided. In that case, note that cell-type labels need to be indicated either directly providing a vector (cell_type_annotations) or by indicating the column name that indicates the cell-type labels (cell_type_column_name). (Anndata: obs object, SingleCellExperiment: colData object).
cell_type_annotations: A vector of the cell type annotations. Has to be in the same order as the samples in single_cell_object.
method: A string specifying the method. Supported methods are the ones in the variable 'deconvolution_methods'
batch_ids: A vector of the ids of the samples or individuals.
bulk_gene_expression: A matrix of bulk data. Rows are genes, columns are samples. Necessary for MOMF and Scaden, defaults to NULL. Row and column names need to be set
verbose: Whether to produce an output on the console.
cell_type_column_name: Name of the column in (Anndata: obs, SingleCellExperiment: colData), that contains the cell-type labels. Is only used if no cell_type_annotations vector is provided.
markers: Named list of cell type marker genes. This parameter is only used by BSeq-sc. The type of gene identifiers (names(markers)) must be the same as the ones used as feature/row names in the single_cell_object.
assay_name: Name of the assay/layer of the single_cell_object that should be used to extract the data
...: Additional parameters, passed to the algorithm used

Value

The signature matrix. Rows are genes, columns are cell types.

Examples

# More examples can be found in the unit tests at tests/testthat/test-b-buildmodel.R
data("single_cell_data_1")
data("cell_type_annotations_1")
data("batch_ids_1")
data("bulk")

single_cell_data <- single_cell_data_1[1:2000, 1:500]
cell_type_annotations <- cell_type_annotations_1[1:500]
batch_ids <- batch_ids_1[1:500]
bulk <- bulk[1:2000, ]

signature_matrix_momf <- build_model(
  single_cell_data, cell_type_annotations, "momf",
  bulk_gene_expression = bulk
)
#> Warning: RGL: unable to open X11 display
#> Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.