My file is like this-

   

      Pcol       Mcol
        P1      M1,M2,M5,M6
        P2      M1,M2,M3,M5
        P3      M4,M5,M7,M6

I want to find the combination of Mcol elements along with Pcol.

Expected output-

    Pcol Mcol        
    P1  M1,M2        
    P2  M1,M2        
    P1  M1,M5        
    P2  M1,M5        
    P1  M1,M6        
    P1  M2,M5        
    P2  M2,M5        
    P1  M2,M6        
    P1  M5,M6        
    P3  M5,M6        
    P2  M1,M3        
    P2  M2,M3        
    P3  M4,M5        
    P3  M4,M7        
    P3  M4,M6        
    P3  M7,M6  

      
I have tried this-

    x <- read.csv("file.csv" ,header = TRUE, stringsAsFactors = FALSE)
    xx <- do.call(rbind.data.frame, 
                  lapply(x$Gcol, function(i){
                    n <- sort(unlist(strsplit(i, ",")))
                    t(combn(n, 2))
                  }))

But it only gives output of combination not the Pcol elements.
Your code was very close we need to add *Pcol* in the output, see below:

    # example data
    x <- read.table(text = " Pcol       Mcol
        P1      M1,M2,M5,M6
        P2      M1,M2,M3,M5
        P3      M4,M5,M7,M6", header = TRUE, stringsAsFactors = FALSE)
    
    
    res <- do.call(rbind,
            apply(x, 1, function(i){
              n <- sort(unlist(strsplit(i[ 2 ], ",")))
              mycomb <- t(combn(n, 2))
              data.frame(Pcol = unname(i[ 1 ]),
                         Mcol = paste(mycomb[, 1], mycomb[, 2], sep = ","))
              })
            )

    #    Pcol  Mcol
    # 1    P1 M1,M2
    # 2    P1 M1,M5
    # 3    P1 M1,M6
    # 4    P1 M2,M5
    # 5    P1 M2,M6
    # 6    P1 M5,M6
    # 7    P2 M1,M2
    # 8    P2 M1,M3
    # 9    P2 M1,M5
    # 10   P2 M2,M3
    # 11   P2 M2,M5
    # 12   P2 M3,M5
    # 13   P3 M4,M5
    # 14   P3 M4,M6
    # 15   P3 M4,M7
    # 16   P3 M5,M6
    # 17   P3 M5,M7
    # 18   P3 M6,M7

Then to address your other question about adding frequency, try:

    res$Freq <- table(res$Mcol)[ res$Mcol ]
    #    Pcol  Mcol Freq
    # 1    P1 M1,M2    2
    # 2    P1 M1,M5    2
    # 3    P1 M1,M6    1
    # 4    P1 M2,M5    2
    # 5    P1 M2,M6    1
    # 6    P1 M5,M6    2
    # 7    P2 M1,M2    2
    # 8    P2 M1,M3    1
    # 9    P2 M1,M5    2
    # 10   P2 M2,M3    1
    # 11   P2 M2,M5    2
    # 12   P2 M3,M5    1
    # 13   P3 M4,M5    1
    # 14   P3 M4,M6    1
    # 15   P3 M4,M7    1
    # 16   P3 M5,M6    2
    # 17   P3 M5,M7    1
    # 18   P3 M6,M7    1

