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Step: Differential Expression Analysis (DEA) using Wilcoxon test

step_dea_wilcox.Rd

Run differential analysis using Wilcoxon analysis via glystats::gly_wilcox(), 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. Only use this method for experiments with 2 groups.

Usage

step_dea_wilcox(
  on = "exp",
  p_adj_method = "BH",
  ref_group = NULL,
  filter_p_adj_cutoff = 0.05,
  filter_p_val_cutoff = NULL,
  filter_fc_cutoff = 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.

ref_group

A character string specifying the reference group. If NULL (default), the first level of the group factor is used as the reference.

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.

...

Additional arguments passed to glystats::gly_wilcox().

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: A table containing the DEA result (if on = "exp", default)

  • dta: A table containing the DTA result (if on = "trait_exp")

  • dma: A table containing the DMA result (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 Wilcoxon test.

  • If the experiment has more than 2 groups but the user wants a specific two-group comparison, ask which two groups to compare and include step_subset_groups(groups = c("A", "B")) before this step.

See also

glystats::gly_wilcox()

Examples

step_dea_wilcox()
#> <step "step_dea_wilcox()"> Differential expression analysis (wilcox)
step_dea_wilcox(on = "trait_exp")  # Differential trait analysis
#> <step "step_dea_wilcox(on = \"trait_exp\")"> Differential trait analysis
#> (wilcox)