$gw6.00033
 X  Sample_Name Chr_No Copy_No Frequence
  1 gw6.00033  chr1:    cn=0         1
 12 gw6.00033  chr2:    cn=0         1
 16 gw6.00033  chr4:    cn=0         1
 20 gw6.00033  chr6:    cn=0         1

   $gw6.0006
  X Sample_Name Chr_No Copy_No Frequence
  26 gw6.0006  chr1:    cn=0         1
  29 gw6.0006  chr10    cn=0         3
  31 gw6.0006  chr11    cn=0         2
  34 gw6.0006  chr13    cn=0         1
  37 gw6.0006  chr15    cn=0         1
  38 gw6.0006  chr16    cn=0         1
  41 gw6.0006  chr2:    cn=0         1
  47 gw6.0006  chr3:    cn=0         1
  57 gw6.0006  chr8:    cn=0         2

sp <- split(cn0, cn0$sample_name)
N <- 22
sp <- lapply(sp, function(DF){
M <- as.numeric(sub("[^[:digit:]]+([[:digit:]]+)[^[:digit:]]*", "\1",     DF$Chr_no))
Chr_no <- sub("[[:digit:]]+[^[:digit:]]*$", "", DF$Chr_no)
Chr_no <- paste0(Chr_no, 1:N)
Chr_no <- ifelse(nchar(Chr_no) == 4, paste0(Chr_no, ":"), Chr_no)
sample_name <- rep(DF$sample_name[1], length(Chr_no))
res <- data.frame(sample_name, Chr_no)
res$Frequence <- 0
res$Frequence[1:N %in% M] <- DF$Frequence
res
  })
   abc <- as.data.frame(t(sapply(sp, '[[', 'Frequence')))
    names(abc) <- sp[[1]]$Chr_no

$gw6.00033
      Sample_Name Chr_No Frequence
    1  gw6.00033  chr1:         1
    2  gw6.00033  chr2:         1
    3  gw6.00033  chr3:         0
    4  gw6.00033  chr4:         1
    5  gw6.00033  chr5:         0
    6  gw6.00033  chr6:         1
    7  gw6.00033  chr7:         0
    8  gw6.00033  chr8:         0
    9  gw6.00033  chr9:         0


$gw6.0006
 Sample_Name Chr_No Frequence
1  gw6.0006  chr1:         1
2  gw6.0006  chr2:         3?
3  gw6.0006  chr3:         2?
4  gw6.0006  chr4:         0
5  gw6.0006  chr5:         0
6  gw6.0006  chr6:         0
7  gw6.0006  chr7:         0
8  gw6.0006  chr8:         1?