Description Usage Arguments Value See Also Examples
The main function, it performs metabolite and wavelet fitting to input NMR spectra,
plots fitting results, posterior distributions for relateive concentrations and peak positions,
and saves output. If the input createDir = TRUE
, a folder name "runBATMAN"
will be created in specified directory, within which, two folders "BatmanInput" and
"BatmanOutput" are created. "BatmanInput" contains the input data files copied from
installed package folder "extdata". The user only needs to modify files in this
folder to change the settings for running batman
. The batman
output files are saved in "BatmanOutput" subfolders.
1 2 3 4 
BrukerDataDir 
The directory of the folder containing 1D Bruker spectral data files.
If not specified, spectral data will be read in from one of the following inputs prioritized
in the order: 
BrukerDataZipDir 
The directory of the folder containing zipped 1D Bruker spectral data files.
If not specified, spectral data will be read in
from one of the following inputs prioritized in the order: 
txtFile 
The .txt file containing spectral data in the format of first column ppm, and
the second column the real part of spectrum. If not specified, spectral data will be read in
from one of the following inputs prioritized in the order: 
rData 
The R data file containing spectral data in the format of first column ppm,
and the second column the real part of spectrum. If not specified, spectral data will be read in
from one of the following inputs prioritized in the order: 
createDir 
If set 
runBATMANDir 
User specified BATMAN work directory, the default is current work directory.
It will only work when 
overwriteDir 
If folder "runBATMAN" exists, set TRUE to overwrite folder. The default is 
figBatmanFit 
Plot metabolites and wavelets fit if set 
listMeta 
Individual metabolite fit will also be shown in the plot if set 
figRelCon 
Plot posterior samples of the relative concentration for fitted
metabolites with 95% credible interval if set TRUE. The default is 
figMetaFit 
If set 
showPlot 
If set 
It returns a data list with the following objects:
specTitle 
A matrix (2 \times n) containing the spectrum number in its first row and the corresponding title of the spectrum in its second row. 
sFit 
A matrix t \times 5n of BATMAN fit results (down sampled). For 1 spectrum, it is a matrix with 5 columns: [ppm, original spectrum, metabolites fit, wavelets fit, overall fit]. The "overall fit" is the posterior mean of the BATMAN fit results after MCMC burn in iterations. Certain numbers of burn in iterations are used at the beginning of an MCMC run for finding a good starting point. n is the number of spectra, and t is the number of data points in each spectrum. 
sFitHR 
A matrix t \times 3n of BATMAN fit results in the original resolution (without down sample). For 1 spectrum, it is a matrix with 3 columns: [ppm, original spectrum, metabolites fit]. n is the number of spectra, and t is the number of data points (without down sample) in each spectrum. 
beta 
A matrix (m \times n) containing the posterior means of relative concentrations for m fitted metabolites and n spectra after burn in. 
betaSam 
A matrix (m \times (s*n)) containing (for the first spectrum) s posterior samples of the relative concentrations in its rows. m is the number of fitted metabolites. n is the number of spectra analyzed. The subsequent columns contain the same format of data for the rest n1 spectra. 
betaCI 
A matrix (m \times 2n) containing the 95% credible interval of the relative concentrations for m fitted metabolites. Every pair of columns is for one spectrum. 
metaTemp 
A matrix (t \times (m*n)) containing the posterior means of m fitted metabolite templates in its columns (down sampled) after burn in. n is the number of spectra analyzed and t is the number of data points in each spectrum. 
metaTempHR 
A matrix (t \times (m*n)) containing the posterior means of m fitted metabolite templates in its columns (without down sample) after burn in. n is the number of spectra analyzed and t is the number of data points (without down sample) in each spectrum. 
metaFitSam 
A matrix (t \times (s*n)) containing s posterior samples of total metabolites fit during MCMC iterations in its columns. n is the number of spectra analyzed and t is the number of data points in each spectrum. The remaining n1 spectra metabolites fit results are saved in the same sequence in subsequent columns. 
metaIndFitSam 
A matrix (t \times (m*s*n)) containing s posterior samples of m individual metabolites fit during MCMC iterations in its columns. n is the number of spectra analyzed and t is the number of data points in each spectrum. The remaining n1 spectra results are saved in the same sequence in subsequent columns. 
thetaSam 
A matrix (t \times (s*n)) containing s samples of wavelet fit during MCMC iterations in its columns. n is the number of spectra analyzed. The remaining n1 spectra wavelet fit results are saved in the same sequence in subsequent columns. 
delta 
A matrix (M \times n) containing posterior means of M multiplets ppm shift of fitted metabolites in its rows. M is the sum of all multiplets in the fitted metabolts. Each column of the matrix corresponds to one spectrum. If only 1 spectrum is analyzed, delta is a column vector. 
deltaSam 
A matrix (s \times (M*n)) containing the posterior samples of multiplets ppm shift. Every M columns correspond the shift posterior samples of M multiplets for one spectrum. M is the sum of all multiplets in the fitted metabolts and n is the number of spectra analyzed. 
outputDir 
The directory of output folder with all the output result files. 
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61  library(batman)
## Run BATMAN
if(interactive()) bm<batman()
## This will create the folder "runBATMAN" in current working directory,
## within the folder "runBATMAN", a subfolder "BatmanInput" contains all the
## input files batman uses. Users can modify "metabolitesList.csv",
## "batmanOptions.txt" and so on to change the settings of batman.
## Please check "BatmanInput" for details on how to adjust input parameters.
########################################################################
## The following is an example of what will be displayed in R
## and what value the user could input:
########################################################################
## batman...
## Number of burnin iterations: 4000
## Number of postburnin iterations: 100
##
## The template file used is
## 1: The default template of multiplets in multi_data.csv file.
##
## Loading multi_data.csv...
## Percentage completed...
##   0%
## Size of each spectrum is 393.
## Size of metabolite list is 22.
## Constructing chain data structure...
## time used is 0 seconds.
## Running MCMC...
## ===================================================  80%
## time used for burnin is 76 seconds.
## ================================================================== 100%
## time used is 95 seconds.
## saving posteriors...
##
## time elapsed
## 95.61
## second.
## Reading in saved data in folder
## .../user_specified_dir/runBATMAN/BatmanOutput/07_Dec_17_19_18
## Completed.
########################################################################
## Alternatively if more than 1 spectrum are included without using fixed effect
## (in batmanOptions.txt file, set
## "Same concentration for all spectra (fixed effect) (1/0): 0"),
## user will be asked to input the following parameter:
########################################################################
## How many parallel processes (multicores) do you want to run
## the multispectra analysis?
## (Enter 1 for running them sequentially.)
##
## Parallel processing of multi spectra currently cannot display
## progress bar (or any words), if you input is > 1, please be patient
## for the results :)
##
## 1: 2 ## user input
## time elapsed
## 78.79
## second.
## Reading in saved data in folder
## .../user_specified_dir/runBATMAN/BatmanOutput/07_Dec_17_35_53
## Completed.
########################################################################

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.