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Run all Downstream analysis pipeline

run_de_pipeline.Rd

Uses the edgeR differentiall expression results and the formatted Deseq2Dataset Performs volcano_plot.R which filters for the chosen log2fc and pval_adj

Usage

run_de_pipeline(
  dds_object,
  edgeR_results,
  deg_log2fc_thresh = 1,
  deg_pval_adj_thresh = 0.05,
  vol_plot_lower_xlim = -10,
  vol_plot_upper_xlim = 10,
  cartesian_step = 5,
  ora_convert_ids = FALSE,
  ora_pval_adj_threshold = 0.05,
  orgdb = org.Hs.eg.db,
  ensembl_dataset = "hsapiens_gene_ensembl"
)

Arguments

dds_object

A formatted DESeq2 object where each sample and its counts are aligned with the respective metadata in @colData.

edgeR_results

dataframe of log2fc results from edge

deg_log2fc_thresh

absolute value cutoff of log2fc

deg_pval_adj_thresh

pvalue cutoff for initial log2fc values

vol_plot_lower_xlim

Numeric value specifying the lower limit of the x-axis. Should be less than 0. For example, -5.

vol_plot_upper_xlim

Numeric value specifying the upper limit of the x-axis. Should be greater than 0. For example, 5.

cartesian_step

Numeric value specifying the interval between x-axis ticks.

ora_convert_ids

Boolean option to convert the gene IDs from Ensemble to External format

ora_pval_adj_threshold

pvalue cutoff of the over-representation test

orgdb

An organism-specific annotation database used to facilitate gene identifier conversion, such as org.Hs.eg.db for human or org.Mm.eg.db for mouse.

ensembl_dataset

Character string specifying the Ensembl dataset used for annotation. For example, "hsapiens_gene_ensembl" for human genes.

Value

A list of the following objects

  • filtered_results: The initial filtering of DEGs log2fc and pval_adj_threshold

  • volcano_plots: visualization of the filtered results on a volcano plot

  • ora_up_raw: Result of the over-representation analysis on upregulated DEGs via clusterProfiler

  • ora_down_raw: Result of the over-represenation analysis on downregulated DEGs via clusterProfiler

  • unpacked_results_up: unpacked results table consisting of a nested list of ORA results on the upregulated DEGs

  • unpacked_results_down: unpacked results table consisting of a nested list of ORA results on the down-regulated DEGs