R Under development (unstable) (2024-08-15 r87022 ucrt) -- "Unsuffered Consequences"
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> library(ClassComparison)
Loading required package: oompaBase
> 
> suppressWarnings( RNGversion("3.5.3") )
> set.seed(782562)
> betaPerc <- 0.10
> nGenes <- 1000
> alpha <- 0.2
> nUnif <- trunc(nGenes*(1-betaPerc))
> pvals <- c(runif(nUnif), rbeta(nGenes-nUnif, alpha, 1))
> fit <- Bum(pvals)
> 
> fit@ahat
[1] 0.1645129
> fit@lhat
[1] 0.9184144
> fit@pihat
[1] 0.9318363
> 
> fdr <- 0.2
> countSignificant(fit, alpha=fdr, by="FDR")
[1] 46
> picked <- selectSignificant(fit, alpha=fdr, by="FDR")
> 
> truth <- rep(c("Null", "Real"), times=c(nUnif, nGenes-nUnif))
> 
> table(truth, byFDR=picked)
      byFDR
truth  FALSE TRUE
  Null   895    5
  Real    59   41
> 
> conf <- 0.80
> countSignificant(fit, alpha=conf, by="EmpiricalBayes")
[1] 30
> epicked <- selectSignificant(fit, alpha=conf, by="EmpiricalBayes")
> 
> table(truth, EB=epicked)
      EB
truth  FALSE TRUE
  Null   900    0
  Real    70   30
> 
> table(byFDR=picked, EB=epicked)
       EB
byFDR   FALSE TRUE
  FALSE   954    0
  TRUE     16   30
> 
> # unknown method
> try( countSignificant(fit, by="HandWaving") )
Error in match.arg(by, c("FDR", "FalseDiscovery", "falsediscovery", "EmpiricalBayes",  : 
  'arg' should be one of "FDR", "FalseDiscovery", "falsediscovery", "EmpiricalBayes", "empiricalbayes"
> 
> # out of range
> try( b <-  Bum(rnorm(1000)) )
Error in Bum(rnorm(1000)) : all p-values must be between 0 and 1
> try( b <- Bum(c(pvals, 1.1)) )
Error in Bum(c(pvals, 1.1)) : all p-values must be between 0 and 1
> 
> # bad input type
> try( b <- Bum(LETTERS) )
Error in Bum(LETTERS) : all p-values must be between 0 and 1
> try( b <- Bum(factor(LETTERS) ))
Error in if (any(pvals < 0) || any(pvals > 1)) { : 
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In Ops.factor(pvals, 0) : '<' not meaningful for factors
2: In Ops.factor(pvals, 1) : '>' not meaningful for factors
> 
> proc.time()
   user  system elapsed 
   0.48    0.04    0.51