adjust_DE_cutoffs

Utility function to adjust mean expression, FDR, and log2FC cutoffs of the database of DEGs inputted into DEET.

Abstract of Manuscript. Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user’s gene lists, aiding in hypothesis generation and data-driven literature review. Sokolowski, Dustin J., et al. "Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression." Nucleic Acids Research Genomics and Bioinformatics (2023).

Dustin Sokolowski

DEET

Differential Expression Enrichment Tool

Jedid Ahn

Lauren Erdman

Kai Ellis

Huayun Hou

Anna Goldenberg

Michael Wilson

adjust_DE_cutoffs function

<dl><dt>DEET_combined</dt>
<dd>The databank of the differential expression enrichment tool.
Appropriate inputs here are "DEET_example_data" stored within DEET, the "DEET_combined.rda" file
from the DEET stable repositoy found at X, and the DEET database developmental repository found at Y.
The DEET_dataset is a named list where details of it's structure can be found ?DEET_example_data.</dd>
<dt>redo_pathways_instructions</dt>
<dd>Boolean value specifying whether to print the instructions
required to update all pathway enrichments based on new DE cutoffs.</dd>
<dt>baseMean</dt>
<dd>Change the mean-expression cutoff.</dd>
<dt>abslog2FoldChange</dt>
<dd>Change the log2 Fold-change cutoff.</dd>
<dt>padj</dt>
<dd>Change the FDR-adjusted p-value cutoff.</dd></dl>

Arguments

Author

adjust_DE_cutoffs — adjust_DE_cutoffs

<dl>

<dt>DEET_combined</dt>
<dd>The databank of the differential expression enrichment tool.
Appropriate inputs here are "DEET_example_data" stored within DEET, the "DEET_combined.rda" file
from the DEET stable repositoy found at X, and the DEET database developmental repository found at Y.
The DEET_dataset is a named list where details of it's structure can be found ?DEET_example_data.</dd>


<dt>redo_pathways_instructions</dt>
<dd>Boolean value specifying whether to print the instructions
required to update all pathway enrichments based on new DE cutoffs.</dd>


<dt>baseMean</dt>
<dd>Change the mean-expression cutoff.</dd>


<dt>abslog2FoldChange</dt>
<dd>Change the log2 Fold-change cutoff.</dd>


<dt>padj</dt>
<dd>Change the FDR-adjusted p-value cutoff.</dd>

</dl>

adjust_DE_cutoffs: adjust_DE_cutoffs

Description

Usage

Value

Arguments

Author

Examples