getFc gets the fold changes. getHr gets the hazard ratios. getMeans gets the means. getPvals gets the p values. getPostProbs get the posterior probabilities. getSignif gets the pvalues or the posterior probabilities depending on the approach (frequentist or bayesian) that was used when the epheno object was created. getSummaryDif gets fold changes and hazard ratios. lofFcHr gets the fold changes and hazard ratios after log scaling. p.adjust.method gets the p value adjustment method that was used when creating the object. phenoClass returns a data.frame telling the class (ordinal, continuous, categorical or survival) of each phenotype. phenoNames gets the phenotype names. approach gets the approach that was used (either frequentist or bayesian).
getEs returns ES (enrichment scores) getEsSim returns simulated ES (needed to compute pvals), getNes returns NES (normalized enrichment scores) and getFcHr returns the fold changes or hazard used to compute the ES, simulated ES and NES.
Returns an object containing the names of the variables that were tested when the epheno object was created. Will return an object of class list. Variables of the same type (categorical, survival, etc) will be in the same slot of the list. The slot names are the types of the variables.
Computes the enrichment scores and simulated enrichment scores for each variable and signature. An important parameter of the function is logScale. Its default value is TRUE which means that by default the provided scores (i.e. fold changes, hazard ratios) will be log scaled. Remember to change this parameter to FALSE if your scores are already log scaled. The getEs, getEsSim, getFc, getHr and getFcHr methods can be used to acces each subobject. For more information please visit the man pages of each method.
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