I am working with two data frames both with 20502 rows, and I want to preform a t.test with the 1st row of one data frame and the 1st of the other data frame and so one until the 20502 row of the two data frames.
ps: I have missing values (NA) in my data frames
If I'm understanding what you're doing correctly, this isn't the typical way to use data.frames - typically, columns should stand on their own as variables, not rows, and the host of data.frame tools available makes use of this assumption. That being said, for data.frames A and B below...
A <- as.data.frame(matrix(1:12,nrow=3,ncol=4))
A
## V1 V2 V3 V4
## 1 1 4 7 10
## 2 2 5 8 11
## 3 3 6 9 12
B <- as.data.frame(matrix(2:13,nrow=3,ncol=4))
B
## V1 V2 V3 V4
## 1 2 5 8 11
## 2 3 6 9 12
## 3 4 7 10 13
...what you'd like to do is a 2-sample t-test of c(1,4,7,10) vs. c(2,5,8,11), etc for each row, all the way down. You could get there with
pvals <- rep(NA, nrow(A))
for(i in 1:nrow(A)) pvals[i] <- t.test(A[i,],B[i,])$p.value