Tests input parameters for functions

validate_input_parameters_bulk(
  SCEs = "placeholder",
  dataset_names = "placeholder",
  celltype = "placeholder",
  celltype_correspondence = "placeholder",
  output_path = "placeholder",
  range_downsampled = "placeholder",
  celltypeIDs = "placeholder",
  sampled = "placeholder",
  sampleIDs = "placeholder",
  bulkDE = "placeholder",
  bulk_cutoff = "placeholder",
  pvalue = "placeholder",
  Nperms = "placeholder",
  fontsize_axislabels = "placeholder",
  fontsize_axisticks = "placeholder",
  fontsize_title = "placeholder",
  fontsize_legendlabels = "placeholder",
  fontsize_legendtitle = "placeholder",
  plot_title = "placeholder"
)

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: the cell type we are focusing on (name as it appears in cell type sub-directory name)
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.
output_path: A clean directory path where down-sampled outputs and plots will be saved (should contain no subdirectories).
range_downsampled: vector or list containing values which the data will be downsampled at, in ascending order
celltypeIDs: A character vector specifying the column name in each SCE that denotes cell type identity (in order of SCEs).
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).
bulkDE: DGE analysis output for a bulk RNA-seq dataset (e.g., LFSR.tsv): rows (rownames) should be the genes, columns should be tissues, and entries should be significance levels
bulk_cutoff: Proportion (0–1) of bulk tissues in which a gene must be differentially expressed to be considered (e.g., 0.9 selects DEGs found in ≥90% of tissues).
pvalue: P-value threshold for defining DEGs in the bulk dataset.
Nperms: Number of permutations to perform for each down-sampling level. Default is 20.
fontsize_axislabels: Font size for axis labels in plot
fontsize_axisticks: Font size for axis tick labels in plot
fontsize_title: Font size for plot title
fontsize_legendlabels: Font size for legend labels in plot
fontsize_legendtitle: Font size for legend title in plot
plot_title: Plot title Checks all bulk analysis parameters are specified correctly