batmanOptions.txt |
Option file to be used by batman . A copy of this
file in the output directory is used for batmanrerun .
The parameters in batmanOptions.txt file are explained here with example
input values. The parameters have to be listed in the particular order given here,
and do not leave empty lines in between except beginning with the comment character "%".
Please note that for version 1.0.9 and later, one more input line,
"Use specified chemical shift for spectra (chemShiftperSpectra.csv) file (1/0): 0",
is added at the end of this file.
For earlier version users updated to this version, running batman will
add the above input line at the end of the file if missing.
ppmRange - ppm ranges for analysis: (1.2, 1.6) (2.1, 2.8)
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. Note that, very small number of spectra variables
may cause error in wavelet analysis, do not give very narrow ppm ranges and also check the "Down sampling:"
factor below, which used together, may also left very small number of spectra variables.
specNo - Ranges of spectra number to be included (e.g. 1,3-4 etc.): 1-3, 5
negThresh - Truncation threshold for negative intensities: -0.5
scaleFac - Intensity scale factor: 20000
downSamp - Down sampling factor: 3
Integer, number of spectra variable will be reduced by the factor of
the input parameter, 3, in this case. For the example shown, the spectra variables
with the index 1:3:end will be used for analysis.
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: 4000
Integer, this is the number of burn-in iterations. The number of iterations
after burn in will be asked when running batman . If changing
the range of spectrum causing fitting results inconsistent, this indicates that the burn in
stage hasn't found the best chemical shift. User may need to increase burn in iterations or reduce
prior truncation on ppm shift for each multiple (adjust parameter "rdelta" below or use "csFlag" function).
nItPostBurnin - Number of post-burn-in iterations: 1000
multFile - Choose template of multiplets file from options below: 2
Integer, choose a template file from the following options:
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: 5
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
a - Gamma-distributed with shape a: 0.00001
b - Gamma-distributed with scale b: 0.000000001
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): 0.1
muVar_prop - Variance of proposal distribution for mu in ln(Hz): 0.002
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): 0.0001
For peak width, γ, in Hz of metabolite m, the model for
γ is \ln(γ)= μ + ν_m
where μ is the spectrum wide average log-peakwidth and
ν_m is a random effect on metabolite deviation from μ.
The mean of each prior on ν_m is 0. Set the variance of the prior on
ν_m to 0 to turn off the random effect on peak width to keep peaks at
the same width. The user can keep the proposal variance parameters unchanged
for most of the case.
tauMean - mean of the prior on tau: -0.01
tauPrec - inverse of variance of prior on tau: 2
rdelta - Truncation of the prior on peak shift (ppm): 0.030
Prior of the truncation on ppm shift for all multiplets, individual prior
for each multiplet can be changed in the "multi_data.csv" file. Increase this
parameter to allow multiplets to shift more. Please note, increasing this value may need more burn in
iterations to find the best chemical shift for multiplets.
csFlag - Specify chemical shift for each multiplet in each spectrum?
(chemShiftperSpectra.csv file) (Yes - 1 / No - 0): 0
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multi_data.csv |
Multiplet template parameters file, obtained from the online
Human Metabolome Database (HMDB) version 2.5. The user can modify the parameters in
the template file and specify ppm positions, and normal distribution truncation of ppm
shift parameters (a positive value applied as +/- on the distribution).
The columns are:
Metabolite : The name of metabolite the multiplets belongs to.
pos_in_ppm : The ppm position of the center of the multiplets.
Refer to the next two parameters for more explanation.
If the next parameter "couple_code" was set to "-1" (empirical multiplet),
this corresponds to the ppm position of the "0" Hz offset of the "J_constant".
If the "couple_code" was set to "-2" (raster multiplet),
this corresponds to the ppm position of the center of the raster multiplet. More details of using
empirical multiplet and raster multiplet can be found in the following 3 fields.
couple_code : Coupling code.
0 = singlet,
1 = doublet,
2 = triplet,
3 = quartet,
4 = quintet,
5 = sextet,
6 = septet,
1,1 = doublet of doublets,
1,2 = doublet of triplets,
2,1 = triplet of doublets,
2,2 = triplet of triplets,
1,3 = doublet of quartets,
3,1 = quartet of doublets,
1,1,1 = doublet of doublet of doublets,
2,3 = triplet of quartets,
3,2 = quartet of triplets,
3,3 = quartet of quartets.
If "-1" is inputted here, a user specified empirical multiplet can be created.
An example can be found in file "multi_data_user.csv". If "-2" is inputted here, a raster multiplet with range
specified in ppm in the field "J_constant" is used. Examples can be found in file "multi_data_user.csv".
J_constant : J constant.
If the empirical multiplet is used ("couple_code" is "-1"),
J_constant contains the offsets in Hz for peaks (each peak corresponds to a offset in Hz, offsets are separated by comma)
of a mutiplet positioned at "pos_in_ppm", J_constant/f (f is the magnet frequency in Hz) is the offset of peak in ppm. Note that the spectra are shown in reverse ppm axis, so
a positive offset means peak at higher ppm value, and a negative offset is peak at lower ppm value.
If the raster multiplet is used ("couple_code" is "-2"), the field here requires a two values input (in ppm) separated by comma, which specifies the
range of the raster multiplet in the pure spectrum. Note in this case, the field "Metabolite" will also be the .txt file name
containing the pure spectrum (refer to createPureSpectraTemplate ).
relative_intensity : (previously called no_of_protons) In the ideal case, at full relaxation, it should correspond to the number of protons in each multiplet. If the empirical multiplet ("couple_code" is "-1"), the same number of values (corresponding to each offset in "J_constant"") needed here as peak intensities. In this case, the sum of "relative_intensity" is the number of protons in this multiplet. If the raster multiplet is used ("couple_code" is "-2"), a single value is needed here corresponds to the number of protons in the included raster multiplet at full relaxation.
overwrite_pos : The default is "n" for not overwrite position, and in that case
the value in "pos_in_ppm" is used for each multiplet. If user want to use a different
value from "pos_in_ppm", it should be put in this column.
overwrite_truncation : The default is "n", and the default truncation value is obtained from
the user input truncation on ppm shift (rdelta) in batmanOptions.txt .
If the user wants to use different truncations for specific multiplets, it should be put in this column.
This value will be used to calculate the ppm shift variance value (truncation/5)
for the corresponding multiplets.
Include_multiplet : The default is "1" and all multiplets belong to the listed
metabolites will be used. Set to "0" to exclude certain multiplet(s) from listed metabolite(s).
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