Combining R + awk + bash commands

Question

I want to combine awk and R language. The thing is that I have a set of *.txt files in a specified directory and that I don\'t know the length of the header from the files.

Answer 1

You can use system to run an external program from R.

system("gawk --version", intern=TRUE)

Answer 2

Besides Vincent's hint of using system("awk ...", intern=TRUE), you can also use the pipe() function that is part of the usual text connections:

R> sizes <- read.table(pipe("ls -l /tmp | awk '!/^total/ {print $5}'"))
R> summary(sizes)
       V1          
 Min.   :       0  
 1st Qu.:     482  
 Median :    4096  
 Mean   :   98746  
 3rd Qu.:   13952  
 Max.   :27662342  
R> 

Here I am piping a command into awk and then read all the output from awk, that could also be a single line:

R> cmd <- "ls -l /tmp | awk '!/^total/ {sum = sum + $5} END {print sum}'"
R> totalsize <- scan(pipe(cmd), quiet=TRUE)
R> totalsize
[1] 116027050
R>