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Preprocess Single Cell and Spatial Data for analysis in spacedeconv

preprocess.Rd

This function prepares SingleCellExperiment or SpatialExperiment objects for downstream analysis by performing a series of preprocessing steps. These steps include converting non-SpatialExperiment objects to SingleCellExperiment format, filtering based on UMI counts, optionally removing mitochondrial genes, and ensuring data integrity.

Usage

preprocess(
  object,
  min_umi = 500,
  max_umi = NULL,
  assay = "counts",
  remove_mito = FALSE
)

Arguments

object

The input object, which can be a SingleCellExperiment, SpatialExperiment, AnnData, or Seurat object. The function will convert AnnData or Seurat objects to SingleCellExperiment if needed.

min_umi

The minimum UMI count threshold for cells or spots to be included in the analysis. This filter helps to remove low-quality observations that might not provide reliable data.

max_umi

The maximum UMI count threshold, used to exclude cells or spots with extremely high UMI counts. This parameter is optional.

assay

The name of the assay to use to compute the preprocessing Default is "counts"

remove_mito

A logical flag indicating whether mitochondrial genes should be removed from the dataset.