delete cols

numCol = 1500
numRow = 3000
mat = matrix(rnorm(numRow*numCol), numRow)
a = ifelse(runif(numCol) < 0.1, NA, rnorm(numCol))
b = ifelse(runif(numCol) < 0.1, NA, rnorm(numCol))

for_ver = function(mat, a, b){
  loc_nonNA = which(!is.na(a)&!is.na(b))
  mat = mat[,loc_nonNA]
  a=a[loc_nonNA]
  b=b[loc_nonNA]
  for (i in 1:nrow(mat))
       mat[i, ]=(mat[i, ]-a)/b
  mat
}

sweep_ver = function(mat, a, b){
  loc_nonNA = which(!is.na(a)&!is.na(b))
  mat = mat[,loc_nonNA]
  a=a[loc_nonNA]
  b=b[loc_nonNA]
  mat=sweep(mat, 2, a, '-')
  mat=sweep(mat, 2, b, '/')
  mat
}

scale_ver = function(mat, a, b){
  loc_nonNA = which(!is.na(a)&!is.na(b))
  mat = mat[,loc_nonNA]
  a=a[loc_nonNA]
  b=b[loc_nonNA]
  mat=scale(mat, a, b)
  mat
}

sweep_ver2 = function(mat, a, b){
  mat=t(na.omit(t(rbind(mat, a, b))))
  a=mat[nrow(mat)-1, ]
  b=mat[nrow(mat), ]
  mat=mat[1:(nrow(mat)-2), ]
  mat=sweep(mat, 2, a, '-')
  mat=sweep(mat, 2, b, '/')
  mat
}

scale_ver2 = function(mat, a, b){
  mat=t(na.omit(t(rbind(mat, a, b))))
  a=mat[nrow(mat)-1, ]
  b=mat[nrow(mat), ]
  mat=mat[1:(nrow(mat)-2), ]
  mat=scale(mat, a, b)
  mat
}

apply_ver = function(mat, a, b){
  loc_nonNA = which(!is.na(a)&!is.na(b))
  t(apply(mat, 1, function(x) (x[loc_nonNA] - a[loc_nonNA]) / b[loc_nonNA]))
}

library(data.table)
library(dplyr)
DT = data.table(mat)
data_table_ver = function(DT, a, b){
  loc_nonNA = which(!is.na(a)&!is.na(b))
  DT %>% select(loc_nonNA) %>%
    scale(a[loc_nonNA], b[loc_nonNA])
}

library(rbenchmark)
benchmark(for_ver(mat, a, b), sweep_ver(mat, a, b), scale_ver(mat, a, b),
  sweep_ver2(mat, a, b), scale_ver2(mat, a, b), apply_ver(mat, a, b),
  data_table_ver(DT, a, b),
  columns = c("test", "replications", "elapsed", "relative"),
    order = "relative", replications = 20)
#                       test replications elapsed relative
# 1       for_ver(mat, a, b)           20    3.03    1.000
# 6     apply_ver(mat, a, b)           20    3.80    1.254
# 3     scale_ver(mat, a, b)           20    5.10    1.683
# 2     sweep_ver(mat, a, b)           20    5.18    1.710
# 7 data_table_ver(DT, a, b)           20    6.04    1.993
# 4    sweep_ver2(mat, a, b)           20    9.75    3.218
# 5    scale_ver2(mat, a, b)           20   10.07    3.323

all.equal(for_ver(mat, a, b), scale_ver(mat, a, b), sweep_ver(mat, a, b),
  scale_ver2(mat, a, b), sweep_ver2(mat, a, b), , data_table_ver(DT, a, b),
  apply_ver(mat, a, b), check.attributes = FALSE) # TRUE