R Under development (unstable) (2023-11-25 r85635 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 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(RCytoGPS)
> 
> sf <- system.file("Examples/JSONfiles", package = "RCytoGPS")
> dir(sf)
[1] "CytoGPS_Result1.json" "CytoGPS_Result2.json" "input1.txt"          
[4] "input2.txt"          
> 
> ## Read one explicitly named JSON file
> temp <- readLGF("CytoGPS_Result1.json", folder = sf)
Reading 1 file(s) from 'D:/RCompile/CRANincoming/R-devel/lib/RCytoGPS/Examples/JSONfiles'.

> class(temp)
[1] "list"
> names(temp)
[1] "source"    "raw"       "frequency" "size"      "CL"       
> temp$source
[1] "CytoGPS_Result1.json"
> class(temp$raw)
[1] "list"
> length(temp$raw)
[1] 1
> names(temp$raw)
[1] "CytoGPS_Result1"
> temp$raw[[1]]$Status
      Status                                                    Karyotype
RN01 Success 44-45,XX,+2,der(2;13)(q10;q10),-6,-8,+12,der(17;18)(q10;q10)
RN02 Success                46,XY,t(14;18)(q32;q21)/46,XY,r(15)/47,XY,+12
RN03 Success                                    47,XY,+12/49,idem,+18,+19
> summary(temp$frequency)
 CytoGPS_Result1.Loss CytoGPS_Result1.Gain CytoGPS_Result1.Fusion
 Min.   :0.00000      Min.   :0.00000      Min.   :0.000000      
 1st Qu.:0.00000      1st Qu.:0.00000      1st Qu.:0.000000      
 Median :0.00000      Median :0.00000      Median :0.000000      
 Mean   :0.02573      Mean   :0.05127      Mean   :0.002688      
 3rd Qu.:0.00000      3rd Qu.:0.00000      3rd Qu.:0.000000      
 Max.   :0.16667      Max.   :0.66667      Max.   :0.166667      
> temp$size
CytoGPS_Result1 
              6 
> 
> ## Read all (well, two) JSON files fom a folder
> temp <- readLGF(folder = sf)
Reading 2 file(s) from 'D:/RCompile/CRANincoming/R-devel/lib/RCytoGPS/Examples/JSONfiles'.

> class(temp)
[1] "list"
> names(temp)
[1] "source"    "raw"       "frequency" "size"      "CL"       
> temp$source
[1] "CytoGPS_Result1.json" "CytoGPS_Result2.json"
> class(temp$raw)
[1] "list"
> length(temp$raw)
[1] 2
> names(temp$raw)
[1] "CytoGPS_Result1" "CytoGPS_Result2"
> temp$raw[[1]]$Status
      Status                                                    Karyotype
RN01 Success 44-45,XX,+2,der(2;13)(q10;q10),-6,-8,+12,der(17;18)(q10;q10)
RN02 Success                46,XY,t(14;18)(q32;q21)/46,XY,r(15)/47,XY,+12
RN03 Success                                    47,XY,+12/49,idem,+18,+19
> temp$raw[[2]]$Status
               Status
RN01 Validation error
RN02          Success
RN03          Success
                                                                        Karyotype
RN01                                                         46,XY,-8,+12,der(14)
RN02 48,XY,t(10;13)(q26;q14),+12,+19/47,XY,t(9;13)(p24;q13),-10,+12,+19/45,XY,-13
RN03                                                    47,XY,+12,dup(14)(q32q32)
> summary(temp$frequency)
 CytoGPS_Result1.Loss CytoGPS_Result1.Gain CytoGPS_Result1.Fusion
 Min.   :0.00000      Min.   :0.00000      Min.   :0.000000      
 1st Qu.:0.00000      1st Qu.:0.00000      1st Qu.:0.000000      
 Median :0.00000      Median :0.00000      Median :0.000000      
 Mean   :0.02573      Mean   :0.05127      Mean   :0.002688      
 3rd Qu.:0.00000      3rd Qu.:0.00000      3rd Qu.:0.000000      
 Max.   :0.16667      Max.   :0.66667      Max.   :0.166667      
 CytoGPS_Result2.Loss CytoGPS_Result2.Gain CytoGPS_Result2.Fusion
 Min.   :0.00000      Min.   :0.00000      Min.   :0.000000      
 1st Qu.:0.00000      1st Qu.:0.00000      1st Qu.:0.000000      
 Median :0.00000      Median :0.00000      Median :0.000000      
 Mean   :0.02247      Mean   :0.04839      Mean   :0.006624      
 3rd Qu.:0.00000      3rd Qu.:0.00000      3rd Qu.:0.000000      
 Max.   :0.25000      Max.   :0.75000      Max.   :0.250000      
> temp$size
CytoGPS_Result1 CytoGPS_Result2 
              6               4 
> 
> ## move about
> home  <- getwd()
> setwd(sf)
> temp <- readLGF( "CytoGPS_Result1.json")
Reading 1 file(s) from '.'.

> temp <- readLGF( "CytoGPS_Result1.json", folder = ".")
Reading 1 file(s) from '.'.

> setwd("..")
> temp <- readLGF(folder = "JSONfiles")
Reading 2 file(s) from 'JSONfiles'.

> setwd(home)
> 
> proc.time()
   user  system elapsed 
   0.45    0.01    0.46