Configuration Profiles

Profiles provide pre-configured defaults for common use-cases. Generate a config file from a profile with:

phenocluster create-config -p <profile> -o config.yaml

Available profiles

Profile	Description	Inference	Stability	Multistate
descriptive	Phenotype discovery only, no statistical inference	off	on	off
complete	All analyses enabled (outcomes, survival, multistate)	on	on	on
quick	Fast iteration for development	on	off	off

Profile details

descriptive

Designed for exploratory phenotype discovery without statistical inference. Outcome analysis and inference are disabled. Stability analysis and survival curves (Kaplan-Meier, Nelson-Aalen) are still computed.

complete

The recommended profile for most analyses. Enables every analysis module: outcome association (logistic regression), survival analysis (Cox PH, log-rank), multistate modelling, and stability assessment. FDR correction is enabled by default.

quick

Designed for fast iteration during development and debugging. Disables the heaviest optional analyses (stability and multistate) while keeping outcome association and survival analysis enabled. Not suitable for publication-quality results.

Customising profiles

The generated config file is a complete YAML that you can edit freely. The profile only sets the initial defaults — you can override any parameter after generation. For example, to start from the complete profile but disable multistate modelling:

phenocluster create-config -p complete -o config.yaml

Then edit config.yaml:

multistate:
  enabled: false