library(TCGAbiolinks)

packageVersion("TCGAbiolinks")

## [1] '2.17.4'

probe.hypo.tumor.samples <-  matrix(
    c(rep(0,10),rep(1,10)),
    nrow = 1,
    dimnames = list(paste0("cg",1),paste0("S",1:20))
)

probe.hypo.normal.samples <-  matrix(
    c(rep(1,10),rep(0,10)),
    nrow = 1,
    dimnames = list(paste0("cg",1),paste0("S",1:20))
)
rowRanges <- GenomicRanges::GRanges(
   "chr1",
   IRanges::IRanges(1000, width = 100),
   strand = "*"
 )
 colData <- S4Vectors::DataFrame(
   Sample_type = c(rep("Tumor",10), rep("Normal", 10)),
   row.names = paste0("S",1:20)
 )
 
hypo.tumor <- SummarizedExperiment::SummarizedExperiment(
          assays = S4Vectors::SimpleList(counts = probe.hypo.tumor.samples),
          rowRanges = rowRanges,
          colData = colData
 )

results <- TCGAanalyze_DMC(
     data = hypo.tumor, 
     p.cut = 0.85,
     groupCol = "Sample_type",
     group1 = "Tumor",
     group2 = "Normal",
     filename = NULL,
     plot.filename = "DMC_tumor_vs_normal_hypo_tumor.pdf"
)

## Group1:Tumor

## Group2:Normal

## Calculating the p-values of each probe...

## 
|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s

## Saving volcano plot as: DMC_tumor_vs_normal_hypo_tumor.pdf

## Saving the results also in a csv file: ./DMR_results_Sample.type_Tumor_Normal_pcut_0.85_meancut_0.2.csv

t(results)

##                              cg1                      
## mean.Tumor                   "0"                      
## mean.Normal                  "1"                      
## mean.Tumor.minus.mean.Normal "-1"                     
## p.value.Tumor.Normal         "1.593791e-05"           
## p.value.adj.Tumor.Normal     "1.593791e-05"           
## status                       "Hypomethylated in Tumor"

results <- TCGAanalyze_DMC(
    data = hypo.tumor, 
    p.cut = 0.85,
    groupCol = "Sample_type",
    group1 = "Normal",
    group2 = "Tumor",
    filename = NULL,
    plot.filename = "DMC_normal_vs_tumor_hypo_tumor.pdf"
)

## Group1:Normal

## Group2:Tumor

## Calculating the p-values of each probe...

## 
|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s

## Saving volcano plot as: DMC_normal_vs_tumor_hypo_tumor.pdf

## Saving the results also in a csv file: ./DMR_results_Sample.type_Normal_Tumor_pcut_0.85_meancut_0.2.csv

t(results)

##                              cg1                        
## mean.Normal                  "1"                        
## mean.Tumor                   "0"                        
## mean.Normal.minus.mean.Tumor "1"                        
## p.value.Normal.Tumor         "1.593791e-05"             
## p.value.adj.Normal.Tumor     "1.593791e-05"             
## status                       "Hypermethylated in Normal"

hypo.normal <- SummarizedExperiment::SummarizedExperiment(
    assays = S4Vectors::SimpleList(counts = probe.hypo.normal.samples),
    rowRanges = rowRanges,
    colData = colData
)

results <- TCGAanalyze_DMC(
    data = hypo.normal, 
    p.cut = 0.85,
    groupCol = "Sample_type",
    group1 = "Tumor",
    group2 = "Normal",
    plot.filename = "DMC_tumor_vs_normal_hypo_normal.pdf"
)

## Group1:Tumor

## Group2:Normal

## Calculating the p-values of each probe...

## 
|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s

## Saving volcano plot as: DMC_tumor_vs_normal_hypo_normal.pdf

## Saving the results also in a csv file: ./DMR_results_Sample.type_Tumor_Normal_pcut_0.85_meancut_0.2.csv

t(results)

##                              cg1                       
## mean.Tumor                   "1"                       
## mean.Normal                  "0"                       
## mean.Tumor.minus.mean.Normal "1"                       
## p.value.Tumor.Normal         "1.593791e-05"            
## p.value.adj.Tumor.Normal     "1.593791e-05"            
## status                       "Hypermethylated in Tumor"

results <- TCGAanalyze_DMC(
    data = hypo.normal, 
    p.cut = 0.85,
    groupCol = "Sample_type",
    group1 = "Normal",
    group2 =  "Tumor",
   plot.filename = "DMC_Normal_vs_Tumor_hypo_normal.pdf"
)

## Group1:Normal

## Group2:Tumor

## Calculating the p-values of each probe...

## 
|                                                    |  0%                      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s

## Saving volcano plot as: DMC_Normal_vs_Tumor_hypo_normal.pdf

## Saving the results also in a csv file: ./DMR_results_Sample.type_Normal_Tumor_pcut_0.85_meancut_0.2.csv

t(results)

##                              cg1                       
## mean.Normal                  "0"                       
## mean.Tumor                   "1"                       
## mean.Normal.minus.mean.Tumor "-1"                      
## p.value.Normal.Tumor         "1.593791e-05"            
## p.value.adj.Normal.Tumor     "1.593791e-05"            
## status                       "Hypomethylated in Normal"