Collate DEGs detected in DGE analysis outputs, across all celltypes in a dataset (datasets/DGE analysis outputs should have common celltypes as specified below)

Collate DEGs detected in DGE analysis outputs, across all celltypes in a dataset (datasets/DGE analysis outputs should have common celltypes as specified below)

gather_celltype_DEGs(
  celltype_correspondence,
  pvalue = 0.05,
  Nperms = 20,
  sampled = c("individuals", "cells"),
  output_path = getwd()
)

Arguments

celltype_correspondence

list of different names specifying each cell type

pvalue

the cut-off p-value used to select DEGs

Nperms

number of permutations of DGE analysis outputs for each sample

sampled

Specifies the unit of down-sampling. Can be either "individuals" or "cells", depending on whether the analysis downsamples across samples or cells. Saves combined list of DEGs (across all cell types) in a subdirectory inside the dataset directory

output_path

path storing the down-sampled DGE analysis for each single-cell dataset, generated for bulk analysis