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setClass("ErrorControl",
representation = representation(
type = "character", # Type of error rate controlled for (FWER, FWER.weak, FDR, FDX, gFWER, perComparison (?))
alpha = "numeric", # Error rate of the procedure
k = "numeric", # Additional parameter for generalized FWE control
q = "numeric" # Additional paramter for FDX control
)
)
##TODO: add slots for "model": formula, link, family
##TODO: write some header, it is the main object that comes out after four weeks of hard work!!
setClass("Mutoss",
representation = representation(
data = "ANY", # Raw data used in model
model = "ANY", # link function,error family and design
description = "character",
statistic = "numeric", # For Z, T or F statistics (maybe different slots?)
hypotheses = "ANY",
hypNames = "character", # Identifiers for the hypotheses tested
criticalValues = "numeric", # Procedure-specific critical values
pValues = "numeric", # Raw p-values. Either imported or calculated with data and model
adjPValues = "numeric", # Procedure-specific adjusted p-values
errorControl = "ErrorControl", # Details of the multiplicity control procedure used.
rejected = "logical", # Logical vector of the output of a procedure at a given error rate
qValues = "numeric", # Storey's estimates of the supremum of the pFDR
locFDR = "numeric", # Efron's local fdr estimates (by which method?)
pi0 = "numeric", # Estimate of the proportion of null hypotheses (by which method?)
confIntervals = "matrix", # Confidence intervals for selected parameters (of which kind? selected how?)
commandHistory = "character"
)
)
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