Create a limma report
create_limma_report.RdGenerates an HTML report based on the results of a limma analysis with splines. The report includes various plots and sections summarizing the analysis results for time effects, average differences between conditions, and interaction effects between condition and time.
Usage
create_limma_report(splineomics, adj_pthresh = 0.05, report_dir = here::here())Arguments
- splineomics
An S3 object of class `SplineOmics` that contains all the necessary data and parameters for the analysis, including:
limma_splines_result: A list containing top tables from differential expression analysis for the three different limma results.meta: A data frame with sample metadata. Must contain a column "Time".condition: A character string specifying the column name in the metadata (meta) that defines groups for analysis. This column contains levels such as "exponential" and "stationary" for phases, or "drug" and "no_drug" for treatments.annotation: A data frame containing feature information, such as gene and protein names, associated with the expression data.report_info: A list containing metadata about the analysis for reporting purposes.
- adj_pthresh
A numeric value specifying the adjusted p-value threshold for significance. Default is 0.05. Must be > 0 and < 1.
- report_dir
A string specifying the directory where the report should be saved. Default is the current working directory.