# SCM Repository

# View of /pkg/batman/inst/extdata/batmanOptions.txt

Parent Directory | Revision Log

Revision

File size: 2274 byte(s)

**120**- (**download**) (**annotate**)*Tue Feb 12 16:30:46 2013 UTC*(6 years, 7 months ago) by*jie*File size: 2274 byte(s)

pkg

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 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. %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% Put each set of ppm range in a pair of parentheses in the same line, %% separate start and end ppm values with a comma, %% separate each set of ppm range with space Include ppm ranges for analysis: (1.2, 1.6) Spectra range to be included: 1 Lower limit for spectrum data point: -0.5 Normalisation factor: 200000 Down sampling: 10 %% 1: yes, 0: no Save metabolites fit same as the original spectrum resolution (1/0): 1 Set seed for random number generation: 25 Stop burn in at iteration: 4000 Save results in every ? iterations: 50 Same concentration for all spectra (fixed effect) (1/0): 0 Rerun iterations: 5000 Start temperature: 1000 Spectrometer frequency (MHz): 600 %% %% Hyper parameters for the global precision priors %% (lambda ~ Gamma(a,b/2)) on wavelet coefficients: a : 0.00001 b : 0.000000001 %% %% Peak width of metabolite m (gamma), the model for gamma is %% log(gamma)= mu + nu_m. where mu is the spectrum wide average log-peakwidth %% and nu_m is a random effect on metabolite deviated from mu. Mean of the prior on mu: 0 Variance of the prior on mu: 0.1 Proposal variance for the Metropolis-Hastings sampler for mu: 0.002 %% set the following parameter to 0 to turn off the random effect on peak width, %% mean of each prior on nu_m is 0, Variance of each of the priors on the nu_m: 0.0025 Proposal variance for the Metropolis-Hastings sampler for each nu_m: 0.0001 %% %% Hyper priors (tau) on negative wavelet coefficient (truncated normal) mean of the prior on tau: -0.01 %% steep is inversely proportional to the variance of the prior on tau steep: 2 %% %% Prior of the truncation of position shift for all multiplets %% individual prior for each multiplet can be changed in the multi_data.csv file rdelta: 0.030 Use specified chemical shift for spectra (chemShiftperSpectra.csv) file (1/0): 0

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

Powered by ViewVC 1.0.0 |