[Bioc-devel] Class for differentially expressed genes?

[Shepherd, Lori]

I would imagine a SummarizedExperiment would be the best option
https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Roman Hillje via Bioc-devel <bioc-devel using r-project.org>
Sent: Monday, March 9, 2020 6:48 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Class for differentially expressed genes?

Hi all,

I was wondering if there is a class for results of differential gene expression analysis. I couldn�t find anything generic. Perhaps it�s too similar to a simple data frame, but I like the idea of having a consistent format. I would imagine something that holds gene names, statistics (logFC, p-value, adjusted p-value), plus optional information, e.g. the percent of cells expressing a gene (in the context of scRNA-seq). This could then be attached to an SCE object (�metadata" slot) to keep all results together. I�m probably making things too complicated and should just use a simple data frame but wanted to be sure that I�m not missing any existing solution. I�d appreciate if you share your advice. Thank you!

Cheers,
Roman
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