deconvolute: Deconvolution

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

Deconvolution

Description

Deconvolution

Usage

deconvolute(
  bulk_gene_expression,
  model = NULL,
  method = deconvolution_methods,
  single_cell_object = NULL,
  cell_type_annotations = NULL,
  batch_ids = NULL,
  cell_type_column_name = NULL,
  normalize_results = FALSE,
  verbose = FALSE,
  assay_name = NULL,
  ...
)

Arguments

bulk_gene_expression	A matrix with the bulk data. Rows are genes, columns are samples.
method	A string specifying the method.
single_cell_object	A matrix 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.
batch_ids	A vector of the ids of the samples or individuals.
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.
normalize_results	Whether the deconvolution results should be normalized. Negative values will be put to 0, and the estimates will be normalized to sum to 1. Defaults to NULL.
verbose	Whether to produce an output on the console.
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.
signature	(Optional) The signature matrix. A signature can be provided for certain methods. If NULL, the signature will be computed internally and will not be saved. If you wish to save the model/signature, use the 'build_model' function instead.

Value

A matrix with the probabilities of each cell-type for each individual. Rows are individuals, columns are cell types.

Examples

# More examples can be found in the unit tests at tests/testthat/test-c-deconvolute.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, ]


deconv_bisque <- deconvolute(
  bulk, NULL, "bisque", single_cell_data,
  cell_type_annotations, batch_ids
)

PelzKo/immunedeconv2 documentation built on Feb. 12, 2025, 4:16 p.m.