Вы можете использовать пакет reshape2:
> reshape2::melt(t(DF[, -1]),
varnames=c("Letter", "row"),
value.name = "Number")
Letter row Number
1 x 1 12
2 y 1 43
3 z 1 23
4 x 2 41
5 y 2 75
6 z 2 32
7 x 3 21
8 y 3 43
9 z 3 60
Данные:
DF = structure(list(Date = c("5-3", "5-1", "9-5"), x = c(12L, 41L,
21L), y = c(43L, 75L, 43L), z = c(23L, 32L, 60L)), .Names = c("Date",
"x", "y", "z"), row.names = c(NA, -3L), class = "data.frame")