I want to apply two functions one function on the block diagonal and the second function on the off-diagonal elements in the data frame

1) outer/arithmetic Create a logical block diagonal matrix indicating whether the current cell is on the block diagonal or not and then use that to take a convex combination of the sin and cos values giving a data.frame as follows:

v <- rep(1:3, c(2, 3, 5))
ind <- outer(v, v, `==`)
ind * sin(df) + (!ind) * cos(df)

2) ifelse Alternately, this gives a matrix result (or use as.matrix on the above). ind is from above.

m <- as.matrix(df)
ifelse(ind, sin(m), cos(m))

3) Matrix::bdiag Another approach is to use bdiag in the Matrix package (which comes with R -- no need to install it).

library(Matrix)

ones <- function(n) matrix(1, n, n)
ind <- bdiag(ones(2), ones(3), ones(5)) == 1

Now proceed as in the last line of (1) or as in (2).

If it's okay for you that the result is stored in a new data frame you could change the order of your instructions and do it like that:

ndf <- cos(df)
ndf[1:2,1:2] <- sin(df[1:2,1:2])
ndf[3:5,3:5] <- sin(df[3:5,3:5])
ndf[6:10,6:10] <- sin(df[6:10,6:10])