The first column is sample names; The remaining columns are read counts from each sample.

The first column are sample names (column name from the count data); The remaining columns are experimental treatments.

The design formula expresses the variables which will be used in modeling. The formula should be a tilde (~) followed by the variables with plus signs between them, e.g., ~ condition1 + condition2

one of the treatment column names from the column data.

A level from the specified treatment column that will be used as the treated group in the DESeq2 analysis.

A level from the specified treatment column that will be used as the untreated group in the DESeq2 analysis.

either "parametric", "local", or "mean" for the type of fitting of dispersions to the mean intensity

the significance cutoff used for optimizing the independent filtering (by default 0.1). If the adjusted p-value cutoff (FDR) will be a value other than 0.1, alpha should be set to that value.