R/validate_input_parameters_bulk.r
validate_input_parameters_bulk.RdTests input parameters for functions
validate_input_parameters_bulk(
bulkDE = "placeholder",
inpath = "placeholder",
range_downsampled = "placeholder",
celltype = "placeholder",
sampled = "placeholder",
bulk_cutoff = "placeholder",
pvalue = "placeholder",
celltype_names = "placeholder",
datasets2 = "placeholder",
celltype_names2 = "placeholder",
Nperms = "placeholder",
fontsize_axislabels = "placeholder",
fontsize_axisticks = "placeholder",
fontsize_title = "placeholder",
fontsize_legendlabels = "placeholder",
fontsize_legendtitle = "placeholder",
plot_title = "placeholder"
)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
path storing the down-sampled DGE analysis for each single-cell dataset, generated for bulk analysis
vector or list containing values which the data will be downsampled at, in ascending order
the cell type we are focusing on (name as it appears in cell type sub-directory name)
downsampling carried out based on what (either "individuals" or "cells")
percentage (proportion between 0 and 1), specified so that we select DEGs common across >= bulk_cutoff of the tissues in the Bulk dataset
the cut-off p-value used to select DEGs (for both, bulk and scRNA-seq datasets)
list of the names specifying cell types in each DGE analysis output (in order they appear in the directory)
list of datasets to be used, with celltype names (in DGE analysis outputs) as celltype_names2
alt. list of the names specifying cell types in each DGE analysis output (in order they appear in the directory), if all are not the same as celltype
number of permutations of DGE analysis outputs for each sample
font size for axis labels in plot
font size for axis tick labels in plot
font size for plot title
font size for legend labels in plot
font size for legend title in plot
plot title Checks all bulk analysis parameters are specified correctly