R Under development (unstable) (2024-04-27 r86487 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(NewmanOmics)
> 
> data(GSE6631)
> HN <- as.matrix(log2(1 + GSE6631))
> HN <- log2((1/19)*median(HN) + HN)
> 
> set.seed(12345)
> picked <- sample(nrow(HN), 2000)
> bankMatrix <- HN[picked, seq(1, ncol(HN), 2)]
> testSet <- HN[picked, seq(2, 6, 2)]
> 
> bs <- bankStat(testSet = testSet, bankMatrix = bankMatrix)
> class(bs) # now a list. Should we create a class?
[1] "list"
> names(bs) # two entries
[1] "nu.statistics" "p.values"     
> summary(bs$nu.statistics)
    Cancer.1            Cancer.2           Cancer.3         
 Min.   :-12.52279   Min.   :-10.7697   Min.   :-11.534449  
 1st Qu.: -0.52482   1st Qu.: -0.5616   1st Qu.: -0.576519  
 Median :  0.29960   Median :  0.2910   Median : -0.077493  
 Mean   :  0.08296   Mean   :  0.1038   Mean   : -0.005766  
 3rd Qu.:  0.99903   3rd Qu.:  0.9687   3rd Qu.:  0.500584  
 Max.   :  5.87033   Max.   :  8.5824   Max.   :  8.547029  
> summary(bs$p.values)
    Cancer.1         Cancer.2         Cancer.3     
 Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
 1st Qu.:0.2999   1st Qu.:0.2872   1st Qu.:0.2821  
 Median :0.6178   Median :0.6145   Median :0.4691  
 Mean   :0.5599   Mean   :0.5560   Mean   :0.4894  
 3rd Qu.:0.8411   3rd Qu.:0.8337   3rd Qu.:0.6917  
 Max.   :1.0000   Max.   :1.0000   Max.   :1.0000  
> 
> bankObj <- createBank(bankMatrix)
> summary(bankObj$rowStats)
      mean             SD              sdEst        
 Min.   :1.954   Min.   :0.01412   Min.   :0.04581  
 1st Qu.:2.470   1st Qu.:0.04578   1st Qu.:0.06954  
 Median :2.778   Median :0.06198   Median :0.07628  
 Mean   :2.745   Mean   :0.07515   Mean   :0.07518  
 3rd Qu.:3.016   3rd Qu.:0.08876   3rd Qu.:0.08209  
 Max.   :3.785   Max.   :0.50759   Max.   :0.08356  
> dim(bankObj$background)
[1] 2000   22
> mean(bankObj$background)
[1] 1.195464e-05
> range(bankObj$background)
[1] -14.91926  14.34338
> 
> bs2 <- bankStat(bankObj, testSet)
> all(bs$nu.statistics == bs2$nu.statistics)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   1.56    0.12    1.67