Last data update: 2014.03.03

R: Read mass spectrometer data
readR Documentation

Read mass spectrometer data

Description

Reads raw mass spectrometer data and parses it into a redux format for further processing.

Usage

read(xfile, masses, blabel, Jpos, kfile = NULL, cafile = NULL,
  dfile = NULL, dlabels = NULL, MS = "ARGUS-VI")

Arguments

xfile

a .csv file with samples and fluence monitor data

masses

a list which specifies the order in which the isotopes are recorded by the mass spectrometer

blabel

a prefix string denoting the blanks

Jpos

a vector of integers denoting the positions of the fluence monitors in the irradiation stack

kfile

a .csv file with the K-interference monitor data (optional)

cafile

a .csv file with the Ca-interference monitor data (optional)

dfile

a .csv file with the detector calibration data (optional)

dlabels

a list which specifies the names of the detectors and the order in which they were recorded by the mass spectrometer

MS

a string denoting the type of mass spectrometer. At the moment only the ARGUS-IV is listed. Please contact the author to add other file formats to Ar-Ar_Redux.

Value

an object of class redux.

Examples

samplefile <-  system.file("Samples.csv",package="ArArRedux")
kfile <- system.file("K-glass.csv",package="ArArRedux")
cafile <- system.file("Ca-salt.csv",package="ArArRedux")
dfile <- system.file("Calibration.csv",package="ArArRedux")
masses <- c("Ar37","Ar38","Ar39","Ar40","Ar36")
dlabels <- c("H1","AX","L1","L2")
X <- read(samplefile,masses,"EXB#",c(3,15),kfile,cafile,dfile,dlabels)
plotcorr(X)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ArArRedux)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ArArRedux/read.Rd_%03d_medium.png", width=480, height=480)
> ### Name: read
> ### Title: Read mass spectrometer data
> ### Aliases: read
> 
> ### ** Examples
> 
> samplefile <-  system.file("Samples.csv",package="ArArRedux")
> kfile <- system.file("K-glass.csv",package="ArArRedux")
> cafile <- system.file("Ca-salt.csv",package="ArArRedux")
> dfile <- system.file("Calibration.csv",package="ArArRedux")
> masses <- c("Ar37","Ar38","Ar39","Ar40","Ar36")
> dlabels <- c("H1","AX","L1","L2")
> X <- read(samplefile,masses,"EXB#",c(3,15),kfile,cafile,dfile,dlabels)
> plotcorr(X)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>