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: list of the input data (elements should be SCE objects)
dataset_names: list of the names of the datasets (as you would like them to appear in the "output_path" directory)
celltype: the cell type we are focusing on (name as it appears in cell type sub-directory name)
celltype_correspondence: list of different names specifying each cell type
output_path: path storing the down-sampled DGE analysis for each single-cell dataset, generated for bulk analysis
range_downsampled: vector or list containing values which the data will be downsampled at, in ascending order
celltypeIDs: list or vector of cell type IDs (in order of SCEs)
sampled: downsampling carried out based on what (either "individuals" or "cells")
sampleIDs: list or vector of sample IDs (in order of SCEs)
bulkDE: DGE analysis output for a bulk RNA-seq dataset: rows (rownames) should be the genes, columns should be tissues, and entries should be significance levels
bulk_cutoff: percentage (proportion between 0 and 1), specified so that we select DEGs common across >= bulk_cutoff of the tissues in the Bulk dataset
pvalue: the cut-off p-value used to select DEGs (for both, bulk and scRNA-seq datasets)
Nperms: number of permutations of DGE analysis outputs for each sample
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