13. frequencyStats: This module computes pairwise statistics for binary declarations specified in the sampleMetadata parameter of config.yml. Test results are saved in <cylinter_output_path>/clustering/final/frequency_stats. This module is automated and configurable (see YAML configures below).
YAML configurations (config.yml)
| Parameter | Default | Description |
|---|---|---|
controlGroups | [“CANCER-FALSE”] | (list of strs) Corresponds to control groups for each binary declaration specified as the fourth elements of sampleMetadata values. |
denominatorCluster | null | (null or int) Cluster to be used as the denominator when computing cluster frequency ratios. Set to null first, then change to cluster number (int) to normalize cluster frequencies to a particular identified cluster if desired. |
FDRCorrection | False | (bool) Whether to compute p-vals and false discovery rate (FDR)-corrected q-vals (True) or compute uncorrected p-vals only (False). |