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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)

ParameterDefaultDescription
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-vals and false discovery rate (FDR)-corrected q-vals (True) or compute uncorrected p-vals only (False).