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Step: Subset Groups

step_subset_groups.Rd

Subset the experiment to specific groups using the group column in sample information. This is useful when downstream steps require exactly two groups for comparison. Usually run after step_preprocess() and before DEA or enrichment steps.

Usage

step_subset_groups(groups = NULL)

Arguments

groups

Group names to keep. If NULL, this step will be skipped.

Value

A glysmith_step object.

Details

Data required:

  • exp: The experiment to subset

Data generated:

  • full_exp: The original experiment before subsetting

This step overwrites exp in the context with the subset experiment.

AI Prompt

This section is for AI in inquire_blueprint() only.

  • Use this step when the experiment has more than 2 groups but the user wants a specific two-group comparison.

  • Ask the user which two groups to compare, and place this step before DEA and enrichment steps.

  • Use the order of the user-provided groups to set factor levels.

Examples

step_subset_groups(groups = c("H", "C"))
#> <step "step_subset_groups(groups = c(\"H\", \"C\"))"> Subset groups