14. frequencyStats: this module is fully automated. It computes pairwise statistics for binary declarations specified in the sampleMetadata parameter of cylinter_config.yml. Test results are saved to a directory called frequency_stats in the clustering subdirectory of the main CyLinter output directory. This path is clustering/2d/frequency_stats in the case of 2D clusterings and clustering/3d/frequency_stats in the case of 3D clusterings.
YAML configurations
| 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-values and false discovery rate (FDR)-corrected q-values (True) or compute uncorrected p-values only (False). |