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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

controlGroups[“CANCER-FALSE”](list of strs) Corresponds to control groups for each binary declaration specified as the fourth elements of sampleMetadata values.
denominatorClusternull(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.
FDRCorrectionFalse(bool) Whether to compute p-values and false discovery rate (FDR)-corrected q-values (True) or compute uncorrected p-values only (False).