R/prop_bulk_DEGs_sc.r
prop_bulk_DEGs_sc.Rd
Obtain overall percentage overlap between DEGs from bulk data (DE across all tissues) and various scRNA-seq datasets, across all common cell types
prop_bulk_DEGs_sc(
bulkDE,
bulk_cutoff = 0.9,
pvalue = 0.05,
sampled = "individuals",
fontsize_axislabels = 12,
fontsize_axisticks = 9,
fontsize_title = 14,
fontsize_legendlabels = 9,
fontsize_legendtitle = 9,
plot_title = "placeholder",
output_path = getwd()
)
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
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).
P-value threshold for defining DEGs in the bulk dataset.
Specifies the unit of down-sampling. Can be either "individuals"
or "cells"
, depending on whether the analysis downsamples across samples or cells.
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 Saves plot showing percentage DEGs from bulk data found in each scRNA-seq dataset, in the appropriate directory
A clean directory path where down-sampled outputs and plots will be saved (should contain no subdirectories).