R/bulk_power_analysis.r
bulk_power_analysis.RdRuns entire bulk RNA-seq power analysis pipeline
bulk_power_analysis(
SCEs,
dataset_names,
celltype_correspondence,
output_path = getwd(),
celltypeIDs = "cell_type",
sampled = "individuals",
sampleIDs = "donor_id",
bulkDE = "placeholder",
bulk_cutoff = 0.9,
pvalue = 0.05,
Nperms = 20,
fontsize_axislabels = 12,
fontsize_axisticks = 9,
fontsize_title = 14,
fontsize_legendlabels = 9,
fontsize_legendtitle = 9,
plot_title = "placeholder"
)A list of SingleCellExperiment (SCE) objects, each representing a scRNA-seq dataset.
A vector of names corresponding to each dataset (as you would like them to appear in output plots).
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.
A directory path where down-sampled outputs and plots will be saved.
A character vector specifying the column name in each SCE that denotes cell type identity (in order of SCEs).
Specifies the unit of down-sampling. Can be either "individuals" or "cells", depending on whether the analysis downsamples across samples or cells.
A character vector specifying the column name in each SCE that represents sample or donor IDs (in order of SCEs).
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
Numeric. 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).
Numeric. P-value threshold for defining DEGs in the bulk dataset.
Number of permutations to perform for each down-sampling level. Default is 20; for quick testing, use a smaller value (e.g., Nperms = 3).
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 all plots in the appropriate directories