To remove columns with some amount of NA, you can use
colMeans(is.na(...))
## Some sample data
set.seed(0)
dat <- matrix(1:100, 10, 10)
dat[sample(1:100, 50)] <- NA
dat <- data.frame(dat)
## Remove columns with more than 50% NA
dat[, which(colMeans(!is.na(dat)) > 0.5)]
## Remove rows with more than 50% NA
dat[which(rowMeans(!is.na(dat)) > 0.5), ]
## Remove columns and rows with more than 50% NA
dat[which(rowMeans(!is.na(dat)) > 0.5), which(colMeans(!is.na(dat)) > 0.5)]