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-boun...@r-project.org> on behalf of Roman Hillje via Bioc-devel <bioc-devel@r-project.org> Sent: Monday, March 9, 2020 6:48 AM To: bioc-devel@r-project.org <bioc-devel@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]]
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