parse.shimadzu: Function for parsing Shimadzy pre-processed .txt file
In HTDA: HTDA (High Throughput Data Analysis)

Description Usage Arguments Details Examples

Function for parsing shimadzu preprocessed .txt file

1	parse.shimadzu(fileName)

fileName

name of .txt file

This function depend on another three function for parsing .txt preprocessed data file i.e Parse.R, extract and FinalTable. This function stores data after parsing into five different clot of class parse.Shimadzu i.e McPeakTable, annotation, Gas Chromatography, mass spectrum and Finaltable . Finaltable slot contains a table represnting GC peaks, Retention time, mass spectrum ion fragmentation peaks for each GC peaks and Total Ion current (TIC).

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (fileName) 
{
    conn = file(fileName, open = "r")
    linn = readLines(conn)
    data <- vector()
    for (i in 1:length(linn)) {
        data <- rbind(data, linn[i])
    }
    read.shimadzu <- Parse(data)
    return(read.shimadzu)
    close(conn)
  }