Step: Reactome Enrichment Analysis on Differentially Expressed Variables

Perform Reactome enrichment analysis on differentially expressed variables using glystats::gly_enrich_reactome(). This step requires one of the DEA steps to be run. Only execute for glycoproteomics experiments with exactly 2 groups. If used for glycomics experiments, the step will be skipped. Use all genes in OrgDb as the background.

Usage

step_sig_enrich_reactome(
  universe = "all",
  plot_type = "dotplot",
  plot_width = 7,
  plot_height = 7,
  ...
)

Arguments

universe: The universe (background) to use for enrichment analysis. One of "all" (all genes in OrgDb), "detected" (detected variables in exp).
plot_type: Plot type for enrichment results ("dotplot", "barplot", etc.).
plot_width: Width of the plot in inches. Default is 7.
plot_height: Height of the plot in inches. Default is 7.
...: Additional arguments passed to glystats::gly_enrich_reactome().

Value

A glysmith_step object.

Details

Data required:

exp: The experiment to perform Reactome enrichment analysis for
sig_exp: The filtered experiment from DEA, generated by step_dea_xxx().

Tables generated:

reactome_enrich: A table containing the Reactome enrichment results.

AI Prompt

This section is for AI in inquire_blueprint() only.

Include this step if needed.
Leave universe to "all" (by default) unless the user explicitly mentions that the background should be the detected variables in exp.
If the experiment has more than 2 groups but the user wants enrichment for a specific two-group comparison, ask which two groups to compare and include step_subset_groups(groups = c("A", "B")) before DEA and enrichment steps.

Examples

step_sig_enrich_reactome()
#> <step "step_sig_enrich_reactome()"> REACTOME enrichment analysis
step_sig_enrich_reactome(plot_type = "barplot")
#> <step "step_sig_enrich_reactome(plot_type = \"barplot\")"> REACTOME enrichment
#> analysis