DESeqResults

DESeqResults is a class in the Bioconductor package DESeq2, designed for storing and manipulating differential gene expression analysis results. It is an S4 object that extends the DataFrame class, inheriting its capabilities for tabular data storage and manipulation. This means DESeqResults objects can hold multiple columns of data, typically including base mean expression, log2 fold change, standard error, test statistic, and adjusted p-values.

The primary purpose of DESeqResults is to present the output of the DESeq2 differential expression testing function in a structured and accessible format. When DESeq2 runs, it generates a DESeqResults object that summarizes the results for each gene or feature tested. This object is crucial for downstream analysis, such as identifying significant genes, creating visualizations like volcano plots, or performing gene set enrichment analyses.

Key slots within a DESeqResults object include columns for the estimated coefficients (e.g., log2 fold change) and their associated statistics, as well as p-values. The object also stores metadata about the analysis, such as the design formula used. It is designed to be easily subsetted, sorted, and filtered, allowing users to focus on genes that meet specific statistical criteria, like a chosen significance threshold for adjusted p-values and a minimum log2 fold change. This class facilitates efficient and organized exploration of differential expression findings.