This function will generate pseudobulk expression matri(ces) from a provided Seurat object, SingleCellExperiment object, or feature x cell matrix. Multiple pseudobulk matrices can be generated across different divisions of a dataset, such as cell types.
Usage
getPseudobulk(
object,
metadata = NULL,
replicate_labels = NULL,
split_labels = NULL,
use_cells = NULL,
min_cells_per_split = 100,
min_cells_per_replicate = 10,
min_replicates_per_split = 6,
min_cells_per_feature = 10,
min_prop_cells_per_feature = 0.1,
filter = TRUE,
pseudobulk = "generate",
use_assay = NULL,
use_layer = NULL,
n_cores = NULL,
verbose = TRUE
)Arguments
- object
An object of class
Seurat,SingleCellExperiment, ormatrix. Data supplied as classmatrixshould be a feature x cell matrix.- metadata
An optional dataframe containing relevant metadata columns corresponding to the data provided to parameter
object. Default =NULLlooks for metadata inobjector other provided inputs.- replicate_labels
A string indicating the name of the metadata column containing the biological replicate labels or a character vector containing the biological replicate labels in order. The biological replicate labels are used to construct/define the pseudobulks. Default =
NULLallowed only whenpseudobulkis "none".- split_labels
A string indicating the name of a column by which to split the cells prior to pseudobulking and performing differential expression (e.g., cell types). Alternately, a character vector containing the split labels for each cell in order. Results will be returned for each unique value indicated by
split_labels. Default =NULLwill generate a single pseudobulk matrix that includes all cells.- use_cells
A vector of cell names to subset the object to prior to subsequent pseudobulk steps. Default =
NULLwill use all cells.- min_cells_per_split
A numeric value indicating the minimum number of cells within one split. Pseudobulk steps will not be performed for splits with fewer cells. Defaults to 100.
- min_cells_per_replicate
A numeric value indicating the minimum number of cells within one replicate for one split. Pseudobulk steps will not be performed for replicates with fewer cells for that split. Defaults to 10.
- min_replicates_per_split
A numeric value indicating the minimum number of distinct replicates represented within one split. Pseudobulk steps will not be performed for splits with fewer replicates. Defaults to 6.
- min_cells_per_feature
A numeric value indicating the minimum number of cells (within a split) with expression of a feature. Pseudobulk expression will not be calculated for features expressed in fewer cells. Defaults to 10.
- min_prop_cells_per_feature
A numeric value indicating the minimum proportion of cells (within a split) with expression of a feature. Pseudobulk expression will not be calculated for features expressed in fewer cells. Defaults to 0.1.
- filter
A Boolean value indicating whether to remove features from the matrices in the output (
TRUE) or simply list features that do not meet the criteria as part of the metadata (FALSE). Defaults toTRUE.- pseudobulk
A string indicating whether to actually pseudobulk ("generate"), or simply apply the filtering thresholds ("none"). Defaults to "generate".
- use_assay
A string indicating the assay to use in the provided object. Default =
NULLwill choose the current active assay forSeuratobjects and thecountsassay forSingleCellExperimentobjects.- use_layer
For
Seuratobjects, a string or vector indicating the layer (previously known as slot) to use in the provided object. Default =NULLwill use thecountslayer.- n_cores
A numeric value indicating the number of cores to use for parallelization. Default =
NULLwill use the number of available cores minus 2.- verbose
A Boolean value indicating whether to use verbose output during the execution of this function. Defaults to
TRUE. Can be set toFALSEfor a cleaner output.