drcme.bin.run_merge_unstable_clusters¶

Script for merging unstable clusters into stable ones.

class drcme.bin.run_merge_unstable_clusters.UnstableClusterMergingParameters(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)[source]¶

Parameter schema for unstable cluster merging

This schema is designed to be a schema_type for an ArgSchemaParser object

UnstableClusterMergingParameters¶
key	description	default	field_type	json_type
input_json	file path of input json file	NA	`InputFile`	str
output_json	file path to output json file	NA	`OutputFile`	str
log_level	set the logging level of the module	ERROR	`LogLevel`	str
components_file	Path to CSV file with sPCA components	NA	`InputFile`	str
post_merge_tau_file	Path to file with cluster membership probabilities after entropy-based merging	NA	`InputFile`	str
post_merge_labels_file	Path to file with cluster labels after entropy-based merging	NA	`InputFile`	str
jaccard_file	Path to file with Jaccard coefficient values after subset-based stability analysis	NA	`InputFile`	str
post_merge_proba_file	Path to file with post-merging cluster membership probabilities	NA	`OutputFile`	str
etypes_file	Path to file with stable e-type assignments	NA	`OutputFile`	str
merge_unstable_info_file	Path to file with merge sequence information	NA	`OutputFile`	str
stability_threshold	Threshold below which clusters are considered unstable	0.5	`Float`	float
outliers	Specimen IDs to exclude from analysis	NA	`List`	int

Functions

main(components_file, post_merge_tau_file, …)

Main runner function for script.

Classes

UnstableClusterMergingParameters([extra, …])

Parameter schema for unstable cluster merging