Downsample the dataset, based either on the individuals or cells, and run DE analysis on each downsampled output. Save results in a dataframe

Downsample the dataset, based either on the individuals or cells, and run DE analysis on each downsampled output. Save results in a dataframe

bulk_downsampling_DGEanalysis(
  SCEs,
  dataset_names,
  celltype_correspondence,
  sampled = c("individuals", "cells"),
  sampleIDs = "donor_id",
  celltypeIDs = "cell_type",
  output_path = getwd(),
  pvalue = 0.05,
  Nperms = 20
)

Arguments

SCEs

A list of SingleCellExperiment (SCE) objects, each representing a scRNA-seq dataset.

dataset_names

A vector of names corresponding to each dataset (as you would like them to appear in output plots).

celltype_correspondence

A named vector that maps a standard cell type label (e.g., "Endo", "Micro") to how that cell type appears in each dataset. Use NA if the cell type is not present in a given dataset.

sampled

Specifies the unit of down-sampling. Can be either "individuals" or "cells", depending on whether the analysis downsamples across samples or cells.

sampleIDs

A character vector specifying the column name in each SCE that represents sample or donor IDs (in order of SCEs).

celltypeIDs

A character vector specifying the column name in each SCE that denotes cell type identity (in order of SCEs).

output_path

A directory path where down-sampled outputs and plots will be saved.

pvalue

the cut-off p-value used to select DEGs

Nperms

number of permutations of DGE analysis outputs for each sample Saves DGE analysis output in the correct directory, to be used by other bulk analysis functions