Question

I have a situation like this:
data.frame1 (240 columns and variable number of rows):

 COL1  COL2  COL3
  a      e    h
  b      f    i
  c      g    l
  d

and data.frame2

 Gene  VAL  
  a    3   
  b    7   
  c    0.5   
  d    3.7
  e    9.08
  f    1.3
 ...   ...

I would like to match and subset each COL of the first data.frame with the data.frame2 (so with the first column of the second data.frame) recursively in order to have the following output:

out:
data.frame3

   COL1   VAL      COL2   VAL
     a     3        e    9.08
     b     7        f    1.3
    ...   ...      ....  ....

any suggestion?

Thanks

Answer 1

This can be done with the function lapply:

data.frame1 <- data.frame(COL1 = letters[1:3], COL2 = c(NA, letters[5], NA))
data.frame2 <- data.frame(Gene = letters[1:6], VAL = rnorm(6))

do.call("cbind",
  lapply(data.frame1,
    function(x) { VAL <- rep(NA, ncol(data.frame1));
      VAL[!is.na(x)] <- data.frame2$VAL[data.frame2$Gene %in% na.omit(x)];
      return(data.frame(x, VAL)) }))

#  COL1.x   COL1.VAL COL2.x  COL2.VAL
#1      a  0.1601884   <NA>        NA
#2      b -0.2035409      e -1.535597
#3      c -0.6661004   <NA>        NA