Import MCA data from Amptek detector (SRIXE)

How to define user function getmca to import multiple spectra from MCA Amptek detector files. List of files is read by list.files function. ldply from package plyr is used to read.table. Dataset is split into subsequent column, some cleaning is done: extracted column name with substr, other parameters from MCA file are extracted to separate dataset. Finally matrix with channels in the first column and spectra in the following are exported to file with write.table. All this is wrapped into function with one parameter: directory name.

getmca <- function(directory ) {
library(plyr)
  file_list <- list.files ()
  dataset <- ldply (file_list, read.table, header=TRUE, sep= "\t")
  l=length (file_list)
  r=rep (file_list, each=2060)
  d1 = as.data.frame (split(dataset, r))
  d2 = data.frame (c( 1:2048 ),d1[ 12:2059 ,1 :l])
  d3= as.matrix (d2)
  # some magic
  class( d3) <- "numeric"
  name=substr (file_list,1 ,nchar (file_list)-4)
  colnames(d3) = c ("Channel", name )
  lt=as.numeric (substr( t(d1 [7,]), 12, 20))
  rt= as.numeric(substr (t( d1[8,]) ,12 ,20 ))
  sd= substr(t (d1[ 9, ]),14 ,32 )
  dead= 100*(rt -lt)/ lt
  sums=colSums (d3[ ,2 :(l+ 1)])
  rate=sums /600
  maxi=apply (d3[ ,2 :(l+ 1)], 2, max)
  description = data.frame (row.names=NULL,name,lt,rt ,sd ,dead,sums,maxi,rate)
  colnames(description) = c ("Name", "LT", "RT" , "Date" , "Dead" , "CS" , "Max" , "Rate")
  write.table (d3, "D:/MCA/data.txt", col.names=F, row.names=F ) 
  }