Question

I need to run an awk script to detect local maxima(peaks) in a spectrum. This spectrum is in the form of two columns in a text file.

This is part of a larger project which will identify whether these peaks represent certain compounds(metabolites really).

I have searched on Google and myriad other places i really cant find anything for running awk scripts in R.

EDIT: The awk script i am using looks something like this-

awk 'BEGIN{dydx = 0;}
{ 
  if(NR > 1)
     { dydx = ($2 - y0)/($1 - x0); } 
  if(NR > 2 && last * dydx < 0)
     { printf( "%.4f  %.4f\n", (x0 + $1)/2, log((dydx<0)?-dydx:dydx)); } ;
  last=dydx; x0=$1; y0=$2
}' /home/chaitanya/Work/nmr_spectra/caffeine/pdata/1/spectrumtext.txt  | awk '$2 > 17'

You can also see this question i had asked yesterday. Please note it is NOT the same question.

Answer 1

you should be able to do

system('your awk command here')

If you have single quotes in your awk command, either do as Hong Ooi suggests and put your awk command in a separate file and then just run that from the system command or escape the single quotes:

> system('echo \'hello guy!\' ')
hello guy!