Default blueprint — blueprint_default • glysmith

This blueprint contains the following steps:

step_ident_overview(): Summarize the experiment using glyexp::summarize_experiment().
step_preprocess(): Preprocess the data using glyclean::auto_clean().
step_plot_qc(when = "post"): Plot QC plots using glyclean::plot_qc().
step_pca(): Principal component analysis using glystats::gly_pca(), and plot the PCA using glyvis::plot_pca().
step_dea_limma(): Differential analysis using glystats::gly_limma().
step_volcano(): Plot a volcano plot using glyvis::plot_volcano().
step_heatmap(on = "sig_exp"): Plot a heatmap using glyvis::plot_heatmap().
step_sig_enrich_go(): Perform GO enrichment analysis using glystats::gly_enrich_go().
step_sig_enrich_kegg(): Perform KEGG enrichment analysis using glystats::gly_enrich_kegg().
step_sig_enrich_reactome(): Perform Reactome enrichment analysis using glystats::gly_enrich_reactome().
step_derive_traits(): Derive traits using glydet::derive_traits().
step_dea_limma(on = "trait_exp"): Differential trait analysis using glystats::gly_limma().
step_heatmap(on = "sig_trait_exp"): Plot a heatmap using glyvis::plot_heatmap().

Usage

blueprint_default(preprocess = TRUE, enrich = TRUE, traits = TRUE)

Arguments

preprocess: Whether to include step_preprocess().
enrich: Whether to include the enrichment steps, i.e. step_sig_enrich_go(), step_sig_enrich_kegg(), and step_sig_enrich_reactome().
traits: Whether to include the derived trait analysis steps, i.e. step_derive_traits() and step_dea_limma(on = "trait_exp").

Value

A glysmith_blueprint object.

Examples

blueprint_default()
#> 
#> ── Blueprint (13 steps) ──
#> 
#> • step_ident_overview()
#> • step_preprocess()
#> • step_plot_qc(when = "post")
#> • step_pca()
#> • step_dea_limma()
#> • step_volcano()
#> • step_heatmap(on = "sig_exp")
#> • step_sig_enrich_go()
#> • step_sig_enrich_kegg()
#> • step_sig_enrich_reactome()
#> • step_derive_traits()
#> • step_dea_limma(on = "trait_exp")
#> • step_heatmap(on = "sig_trait_exp")