I have a table: 
  

      W X Y Z
    A 2 3 4
    A 2 3 6
    B 1 2 3
    C 3 2 1
    B 1 3 4
    B 1 2 2
    
    
    # reproducible data
    table <- read.table(textConnection("W\tX\tY\tZ
                                       A\t2\t3\t4
                                       A\t2\t3\t6
                                       B\t1\t2\t3
                                       C\t3\t2\t1
                                       B\t1\t3\t4
                                       B\t1\t2\t2"), header = TRUE)

I want to combine all rows with same value in Column W, so that it looks like

    W   X  Y     Z
    A   2  3     2,6
    B   1  2,3   3,4,2
    C   3  2     1 

**Note:** All different values of column **W** entries appear as comma separated.
You're looking for the R package 'plyr'

     X1 <- read.table(textConnection("W\tX\tY\tZ
     A\t2\t3\t4
     A\t2\t3\t6
     B\t1\t2\t3 
     C\t3\t2\t1
     B\t1\t3\t4
     B\t1\t2\t2"),header=T)

     library(plyr)

     X2 <- ddply(X1, .(W), summarize,
            Xc=paste(X,collapse=","), 
            Zc=paste(Z,collapse=",") ,
            Yc= paste(Y,collapse=","))


     X2

      W    Xc    Zc    Yc
    1 A   2,2   4,6   3,3
    2 B 1,1,1 3,4,2 2,3,2
    3 C     3     1     2


    X2u <- ddply(X1, .(W), summarize,
       Xc=paste(unique(X),collapse=","), 
       Zc=paste(unique(Z),collapse=",") ,
       Yc= paste(unique(Y),collapse=","))

    X2u
      W Xc    Zc  Yc
    1 A  2   4,6   3
    2 B  1 3,4,2 2,3
    3 C  3     1   2