R Under development (unstable) (2025-05-26 r88238 ucrt) -- "Unsuffered Consequences"
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> library(plasma)
> ## check data sets
> fls <- try(loadESCAdata())
> if (inherits(fls, "try-error")) {
+   stop("Unable to load data from remote server.")
+ }
> ls()
[1] "fls"
> ## make sure we can assemble MultiOmics objects
> MO <- with(plasmaEnv, prepareMultiOmics(assemble, Outcome))
> ## Test summary and plot methods
> summary(MO)
Datasets:
     ClinicalBin ClinicalCont MAF Meth450 miRSeq mRNASeq RPPA
[1,]          53            6 566    1454    926    2520  192
[2,]         185          185 185     185    185     185  185
Outcomes:
   patient_id  vital_status days_to_death    days_to_last_followup
 a3i8   :  1   alive:108    Min.   :   9.0   Min.   :   4.0       
 a3ql   :  1   dead : 77    1st Qu.: 180.0   1st Qu.: 336.5       
 a3y9   :  1                Median : 351.0   Median : 402.5       
 a3ya   :  1                Mean   : 495.2   Mean   : 570.1       
 a3yb   :  1                3rd Qu.: 650.0   3rd Qu.: 696.8       
 a3yc   :  1                Max.   :2532.0   Max.   :3714.0       
 (Other):179                NA's   :108      NA's   :77           
      Days       
 Min.   :   4.0  
 1st Qu.: 232.0  
 Median : 400.0  
 Mean   : 538.9  
 3rd Qu.: 681.0  
 Max.   :3714.0  
                 
> opar <- par(mai = c(1.02, 1.82, 0.82, 0.42))
> plot(MO)
> par(opar)
> ## Make sure we can use the subset operator
> train <- rep(c(TRUE, FALSE), times = c(112, 185-112))
> MO2 <- MO[, train]
> summary(MO2)
Datasets:
     ClinicalBin ClinicalCont MAF Meth450 miRSeq mRNASeq RPPA
[1,]          53            6 566    1454    926    2520  192
[2,]         112          112 112     112    112     112  112
Outcomes:
   patient_id  vital_status days_to_death  days_to_last_followup
 a3i8   :  1   alive:63     Min.   :   9   Min.   :  11.0       
 a3ql   :  1   dead :49     1st Qu.: 157   1st Qu.: 293.5       
 a3y9   :  1                Median : 390   Median : 441.0       
 a3ya   :  1                Mean   : 548   Mean   : 622.2       
 a3yb   :  1                3rd Qu.: 764   3rd Qu.: 721.5       
 a3yc   :  1                Max.   :2532   Max.   :3714.0       
 (Other):106                NA's   :63     NA's   :49           
      Days       
 Min.   :   9.0  
 1st Qu.: 223.2  
 Median : 409.0  
 Mean   : 589.7  
 3rd Qu.: 739.2  
 Max.   :3714.0  
                 
> ## For future reference, show there are no survival differences
> if (require("survival")) {
+   plot(survfit(Surv(Days, vital_status == "dead") ~ train, data = MO@outcome),
+                col=c("cyan4", "magenta"), lwd=3)
+ }
Loading required package: survival
> ## And check that the other argument also works
> MO3 <- MO[c("ClinicalBin", "RPPA"),]
> summary(MO3)
Datasets:
     ClinicalBin RPPA
[1,]          53  192
[2,]         185  185
Outcomes:
   patient_id  vital_status days_to_death    days_to_last_followup
 a3i8   :  1   alive:108    Min.   :   9.0   Min.   :   4.0       
 a3ql   :  1   dead : 77    1st Qu.: 180.0   1st Qu.: 336.5       
 a3y9   :  1                Median : 351.0   Median : 402.5       
 a3ya   :  1                Mean   : 495.2   Mean   : 570.1       
 a3yb   :  1                3rd Qu.: 650.0   3rd Qu.: 696.8       
 a3yc   :  1                Max.   :2532.0   Max.   :3714.0       
 (Other):179                NA's   :108      NA's   :77           
      Days       
 Min.   :   4.0  
 1st Qu.: 232.0  
 Median : 400.0  
 Mean   : 538.9  
 3rd Qu.: 681.0  
 Max.   :3714.0  
                 
> 
> ## Things expected to fail
> ## disorient one of the component datasets.
> badinput <- with(plasmaEnv, assemble)
> badinput$mRNASeq <- t(badinput$mRNASeq)
> pmo <- try( with(plasmaEnv, prepareMultiOmics(badinput, Outcome) ))
Error in FUN(X[[i]], ...) : 
  No matching sample names in dataset 'mRNASeq'.

> 
> proc.time()
   user  system elapsed 
   5.81    0.68    7.87