Step: Differential Expression Analysis (DEA) using Kruskal-Wallis test

Run differential analysis using Kruskal-Wallis analysis via glystats::gly_kruskal(), then filter the experiment to keep only the differentially expressed variables using glystats::filter_sig_vars(). By default, this runs DEA on the main experiment (exp), but can be configured to run on derived traits (trait_exp) or other experiment objects.

Usage

step_dea_kruskal(
  on = "exp",
  p_adj_method = "BH",
  filter_p_adj_cutoff = 0.05,
  filter_p_val_cutoff = NULL,
  filter_fc_cutoff = NULL,
  filter_on = "main_test",
  filter_comparison = NULL,
  ...
)

Arguments

on: Name of the experiment data in ctx$data to run analysis on. Default is "exp" for differential expression analysis. Use "trait_exp" for differential trait analysis. Use "motif_exp" for differential motif analysis.
p_adj_method: A character string specifying the method to adjust p-values. See p.adjust.methods for available methods. Default is "BH". If NULL, no adjustment is performed.
filter_p_adj_cutoff: Adjusted p-value cutoff for filtering.
filter_p_val_cutoff: Raw p-value cutoff for filtering.
filter_fc_cutoff: Fold change cutoff for filtering.
filter_on: Filter on "main_test" or "post_hoc_test" for Kruskal-Wallis results.
filter_comparison: Comparison name for post-hoc filtering.
...: Additional arguments passed to glystats::gly_kruskal().

Value

A glysmith_step object.

Details

Data required:

Depends on on parameter (default: exp)

Data generated:

dea_res: The DEA results (if on = "exp", default)
dta_res: The DTA results (if on = "trait_exp")
dma_res: The DMA results (if on = "motif_exp")
sig_exp: The filtered experiment (if on = "exp", default)
sig_trait_exp: The filtered trait experiment (if on = "trait_exp")
sig_motif_exp: The filtered motif experiment (if on = "motif_exp")

Tables generated:

dea_main_test, dea_post_hoc_test: Tables containing the results (if on = "exp", default)
dta_main_test, dta_post_hoc_test: Tables containing the results (if on = "trait_exp")
dma_main_test, dma_post_hoc_test: Tables containing the results (if on = "motif_exp")

AI Prompt

This section is for AI in inquire_blueprint() only.

Include this step only if the user explicitly asks for Kruskal-Wallis test.

Examples

step_dea_kruskal()
#> <step "step_dea_kruskal()"> Differential expression analysis (kruskal)
step_dea_kruskal(on = "trait_exp")  # Differential trait analysis
#> <step "step_dea_kruskal(on = \"trait_exp\")"> Differential trait analysis
#> (kruskal)