I would like to combine/sum two rows based on rownames to make one row in R. The best route might be to create a new row and sum the two rows together.
Example df:<
You can replace the A row using the standard addition arithmetic operator, and then remove the C row with a logical statement.
df["A", ] <- df["A", ] + df["C", ]
df[rownames(df) != "C", ]
#   V2 V3 V4 V5
# A  7 11  5  8
# B  3  2  7  9
# D  3  2  8  9
For more than two rows, you can use colSums() for the addition.  This presumes the first value in nm is the one we are replacing/keeping.
nm <- c("A", "C")
df[nm[1], ] <- colSums(df[nm, ])
df[!rownames(df) %in% nm[-1], ]
I'll leave it up to you to change the row names. :)
Data:
df <- structure(list(V2 = c(1L, 3L, 6L, 3L), V3 = c(3L, 2L, 8L, 2L), 
    V4 = c(4L, 7L, 1L, 8L), V5 = c(6L, 9L, 2L, 9L)), .Names = c("V2", 
"V3", "V4", "V5"), class = "data.frame", row.names = c("A", "B", 
"C", "D"))
matrix multiply?
> A <- matrix(c(1,0,0,0,1,0,1,0,0,0,0,1), 3)
> A                                        
     [,1] [,2] [,3] [,4]
[1,]    1    0    1    0
[2,]    0    1    0    0
[3,]    0    0    0    1
> A %*% X
     V2 V3 V4 V5
[1,]  7 11  5  8
[2,]  3  2  7  9
[3,]  3  2  8  9
Or using the Matrix package for sparse matrices:
fac2sparse(factor(c(1,2,1,4))) %*% X
aggregate to the rescue:
aggregate(df, list(Group=replace(rownames(df),rownames(df) %in% c("A","C"), "A&C")), sum)
#  Group V2 V3 V4 V5
#1   A&C  7 11  5  8
#2     B  3  2  7  9
#3     D  3  2  8  9