# SCM Repository

# View of /documentation and test/Test4/batmanOptions.txt

Parent Directory | Revision Log

Revision

File size: 3430 byte(s)

**372**- (**download**) (**annotate**)*Thu Sep 14 09:28:32 2017 UTC*(22 months ago) by*jie*File size: 3430 byte(s)

Test4 unzipped files

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Options file for BATMAN %%%%%%%%%%%%%%%%%%%%%%%%% %% There should be no empty line in the file, if line %% %% is not used, please comment the start of the line with %. %% %% Please do not comment or remove any of the parameter input lines. %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% General parameters: %% ppm ranges for analysis: Please put each ppm range in a pair of parentheses in the same line, %% separate start and end ppm values with a comma, and %% separate each set of ppm range with space, e.g. (-0.05,0.05) (1.44,1.52) ppmRange - ppm ranges for analysis: (3.505,3.62) specNo - Ranges of spectra number to be included (e.g. 1,3-4 etc.): 1-31 paraProc - No of parallel processes (multicores) (only 1 core will be used for single spectrum): 7 negThresh - Truncation threshold for negative intensities: -0.5 scaleFac - Intensity scale factor: 900000 downSamp - Down sampling factor: 3 hiresFlag - Save metabolite fit at resolution of original spectrum? (Yes - 1 / No - 0): 1 randSeed - Random number seed: 25 nItBurnin - Number of burn-in iterations: 7000 nItPostBurnin - Number of post-burn-in iterations: 1000 multFile - Choose template of multiplets file from options below: 2 %% 1, The default template of multiplets in multi_data.csv file, %% 2, The user input template of multiplets in multi_data_user.csv file, %% 3, Both the default and user input template of multiplets files. %% thinning - Save MCMC state in every ? iterations: 100 cfeFlag - Same concentration for all spectra (fixed effect)? (Yes - 1 / No - 0): 0 nItRerun - Number of iterations for batmanrerun: 5000 startTemp - Start temperature: 1000 specFreq - Spectrometer frequency (MHz): 600 %% %% Uncatalogued (wavelet) component: %% Hyper parameters for the global precision priors, lambda is inversely proportional to error variance. %% lambda ~ Gamma(a,b/2) on wavelet coefficients: a - Gamma-distributed with shape a: 0.00001 b - Gamma-distributed with scale b: 0.000000001 %% %% Catalogued metabolite component: gamma is the peak width (full width at half max) of metabolite m. %% The model for gamma is ln(gamma)= mu + nu_m, where mu is the spectrum-wide average log-peak width %% and nu_m is a random effect for each metabolite deviating from mu. muMean - Mean of prior on global peak width (mu) in ln(Hz): 0 muVar - Variance of prior on global peak width (mu) in ln(Hz): 0.01 muVar_prop - Variance of proposal distribution for mu in ln(Hz): 0.0002 %% The mean of each prior on nu_m is 0. %% Set variance of prior on peak width offset (nu_m) to 0 to turn off the random effect on peak width: nuMVar - Variance of prior on peak width offset (nu_m) in ln(Hz): 0.0025 nuMVarProp - Variance of proposal distribution for nu_m in ln(Hz): 0.01 %% %% Wavelet truncation: tau is a vector of truncation limits, which sets a lower bound on the wavelets tauMean - mean of the prior on tau: -0.01 tauPrec - inverse of variance of prior on tau: 2 %% %% Global prior on peak shift (truncated Gaussian) %% Note: individual priors for each multiplet can be changed in the multi_data(_user).csv file rdelta - Truncation of the prior on peak shift (ppm): 0.01 csFlag - Specify chemical shift for each multiplet in each spectrum? (chemShiftperSpectra.csv file) (Yes - 1 / No - 0): 1

root@r-forge.r-project.org | ViewVC Help |

Powered by ViewVC 1.0.0 |