fiems_lct_main: LCT Mass Binning
In aberHRML/FIEmspro: Flow In-jection Electrospray Mass Spectrometry Processing: \\ data processing, classification modelling and variable selection in metabolite fingerprinting

Description Usage Arguments Details Value Note Author(s) See Also Examples

Main Routine for ‘Mass Binning’ to nominal mass and ‘Mass Spectrum’ generation in high-throughput Flow Injection Electrospray Ionisation Mass Spectrometry (FIE-MS). This routine reads ANDI NetCDF files (*.cdf) of LCT/Q-ToF *.raw data files converted in the DataBridge program (Dbridge, MassLynx, Micromass).

1 2	fiems_lct_main(my_path,runinfo,y1,y2,y3,y4,limit=0.82, save.file=TRUE,file.name="LCT-mean.RData")

`my_path`	A character string indicating the working directory where `runinfo.csv` file and folder containing `*.cdf`-files are located.
`runinfo`	A `*.csv` file containing at least the following run information (header row): `pathcdf` and `filecdf` . For details, see the description in `Examples` below.
`y1`	A numeric value used for mass spectrum generation: start scan ‘sample’. For details, see the description in `Examples` below.
`y2`	A numeric value used for mass spectrum generation: end scan ‘sample’. For details, see the description in `Examples` below.
`y3`	A numeric value used for mass spectrum generation: start scan ‘background’. For details, see the description in `Examples` below.
`y4`	A numeric value used for mass spectrum generation: end scan ‘background’. For details, see the description in `Examples` below.
`limit`	A numeric value defining the rounding limit for binning m/z-values to nominal mass.
`save.file`	A logical value indicating whether or not to save the results (default is `TRUE`).
`file.name`	A character for saved file name if `save.file` is `TRUE`.

This routine is designed to handle only one MassLynx (Micromass) specific function (e.g. data acquired at one cone voltage). Each *.cdf-file will result in one mass spectrum. Principle in brief: load *.cdf-file (pathcdf and filecdf information in runinfo.csv); bin m/z-values to nominal mass between ‘limit-1’ and ‘limit’; sum up intensities of binned m/z values; generate sample matrix ‘smat’ between scans y1 and y2 and background matrix ‘bmat’ between scans y3 and y4; subtract: mat=smat-bmat; calculate mean of resulting matrix ‘mat’; potential negative values are set to ‘zero’. The implemented timer-function should be accurate for up to 24 hours which could comprise more than 7000 *.cdf-files per experiment.

A list containing the following components:

`mat`	Single matrix [runs x nominal masses] of the full mass range [0:2000] in the ionisation mode.
`runinfo`	Same as argument stored for reference purposes. Additional information for each run like sample name or class can be used for further analysis (e.g. nlda).
`scrng`	A vector of `y1`, `y2`, `y3` and `y4` stored for reference purposes.
`limit`	Same as argument stored for reference purposes.

The returned values are saved by default as LCT-mean.RData in folder my_path. Additionally, single items are saved by default as TEXT files: mat.txt, myparam.txt (containing scrng and limit for reference purposes).

Manfred Beckmann meb@aber.ac.uk

fiems_ltq_main

## Example profiles can be downloaded on the FIEmspro webpage
## 021016Pot-24_LCT_ESI_-.zip must be extracted in folder that defines 'my_path'

## For e.g.
## Not run: my_path <- "D:/Temp/021016Pot-24_LCT_ESI_-"
## The same folder should also contain a 'runinfo' file
## For e.g.
## Not run: runinfo <- "runinfo.csv"
## Process each profile defined in 'runinfo'
## Not run: tmp <- fiems_lct_main(my_path,runinfo,15, 25,50,	60,limit=0.82,
               save.file=TRUE,file.name="LCT-mean.RData")
## End(Not run)

## ===================================================================
## Arguments and matrices are saved in 'my_path', ideally the working 
## directory of the experiment. For explanations regarding input 
## arguments see below ...

# required is a file named by default 'runinfo.csv'
# (comma separated variables, generated in e.g. MS-Excel);
# the structure should be the following to ease data pre-processing:

#    A     |                  B                   |       C         |  D
# injorder | pathcdf                              | filecdf         |batch
#-------------------------------------------------------------------------
#  1       | D:/../Pot-LCT-2001-bc/Test_LCT_ESI_- | 021016MAN10.CDF | 1
#  2       | D:/../Pot-LCT-2001-bc/Test_LCT_ESI_- | 021016MAN11.CDF | 1
# and so on...

#  Columns:
# 'injorder' is injection order of samples (good for investigating drifts)
# 'pathcdf'  is path of folder containing "*.cdf"-files. Each run-sequence
#            or batch of runs might have its own folder.
# 'filecdf'  is the actual filename of an "*.cdf"-file.
# 'batch'    is the number of the batch the run belongs to (good for
#            investigating batch effects)

# In practice the file will contain further information regarding sample name,
# class/group information and probably other meta-data describing a sample.


## LCT Instrument Method for Flow-Injection-ESI-MS (FIE-MS):
## - 1 Function only, either positive or negative ionization mode
## - m/z range: 65.0-1000.0  (default max = 2000)   resolution: 4000
## - 2 min Acquisition

## Infusion Profile (Sketch):
##          _
##         / \
##        /   \
##       /     \_
##      /        \__
## ____/            \______________________________
## 0         0.5          1          1.5          2 [min]
##       |------|               |------|
##      [y1]   [y2]            [y3]   [y4]   [scan reading]
##        sample               background
## Using the above given LCT Instrument Method for FIE-MS
##   the actual scan readings y1 to y4 are used directly:
##       scrange = c(y1,y2,y3,y4)
##       with (ideally):  y2 - y1 = y4 - y3

## Raw data conversion to ANDI NetCDF-file: 
##       DataBridge program (Dbridge, MassLynx, Micromass)