Batman-Output: BATMAN Outputs are Explained Here
In batman: Bayesian AuTomated Metabolite Analyser for NMR spectra
Description
batman and batmanrerun return the results as a data list with the objects described
in their individual function. They also put results in .txt format in a folder named
after the start execution time (date\_month\_hours\_mins\_seconds) within either folder ".../runBATMAN/BatmanOutput"
or folder "extdata" depending on batman input createDir settings.
Value
batman and batmanrerun save their results in the following files in the output folder:
beta_i_rr_j.txt
A column vector (m \times 1) containing the estimated
posterior mean of relative concentrations for m fitted metabolites of spectrum i.
For batman results, j
is 0, and for batmanrerun results, j is 1.
beta_sam_i_rr_j.txt
A matrix (m \times s) with each row containing the s posterior samples of
the relative concentrations for one fitted metabolite of spectrum i.
m is the total number of fitted metabolites. For batman results, j
is 0, and for batmanrerun results, j is 1.
delta_draw_mean_i.txt
A column vector (M \times 1) containing the posterior
mean of M multiplets ppm shift from the pre-set ppm position value in
multi_data.csv or multi_data_user.csv of spectrum i.
delta_sam_i.txt
A matrix (s \times M) containing the posterior samples
of M multiplets ppm shift. Every column correspond the shift posterior samples
of one multiplet for spectrum i. M is the sum of all
multiplets in the fitted metabolites.
L_i.txt
A matrix (t \times M) with each column as the template of one
fitted metabolite for spectrum i before fitting. t
is the number of data points in each spectrum.
lambda_sam_i_rr_j.txt
A column vector (s \times 1)
containing s posterior samples of λ (a scalar global precision
parameter) for spectrum i. For batman results, j is 0,
and for batmanrerun results, j is 1.
metabolitesListUsed.txt
A column vector (m \times 1) containing the
m metabolite names
which have multiplets in/near the ppm region specified in batmanOptions.txt and used in the fitting.
metaFit_sam_i_rr_j.txt
A matrix (t \times s) containing
s posterior samples of total metabolites fit during MCMC iterations in
its columns for spectrum i. t is the number of data points in each spectrum.
For batman results, j is 0, and for batmanrerun results, j is 1.
metaIndFit_sam_i_rr_j.txt
A matrix (t \times (m*s))
containing s posterior samples of m individual metabolites fit in
its columns for spectrum i. t is the number of data points in each
spectrum. Every m columns are the m individual metabolite fit
samples for one posterior sample. For batman results, j
is 0, and for batmanrerun results, j is 1.
metaTemp_i_rr_j.txt
A matrix t \times m) containing the posterior means of
m fitted metabolite templates in its columns (down sampled) after burn in
for spectra i. t is the number of data points in each spectrum.
For batman results, j is 0, and for batmanrerun
results, j is 1.
metaTempHR_i_rr_j.txt
A matrix (t \times m) containing the posterior means of
m fitted metabolite templates in its columns (without down sample) after burn in
for spectra i. t is the number of data points (without down sample)
in each spectrum. For batman results, j
is 0, and for batmanrerun results, j is 1.
MultipletsPpmShifts.txt
A table (M \times n) containing the posterior means
of multiplets ppm shift for M multiplets as its rows. M is the sum of all
multiplets in the fitted metabolites and n is the number of spectra analyzed.
NMRdata_mod_i.txt
A matrix (t \times 2) containing the input
spectrum i in its original resolution. The first column is ppm value,
and the second column is the ith spectrum intensity.
RelCon.txt
A table (m \times n) of the posterior means of relative
concentrations for m fitted metabolites and n spectra.
RelConCreInt.txt
A table (m \times 2n) containing the 95% credible
intervals (2.5% and 97.5%) for the relative concentrations of m
fitted metabolites for n spectra.
specFit_i_rr_j.txt
A matrix (t \times 5) of BATMAN fit
results with five columns as:
[ppm, Original spectrum, Metabolites fit, Wavelet fit, Overall sum]
of spectrum i.
For batman results, j is 0, and for batmanrerun results, j is 1.
specFitHR_i_rr_j.txt
A column vector (t \times 1) of
metabolite fit result in the original resolution for spectrum i. t is the
number of data points (without down sample) in each spectrum.
For batman results, j is 0,
and for batmanrerun results, j is 1.
theta_sam_i_rr_j.txt
A matrix (t \times s) containing
s samples of wavelet fit during MCMC iterations in its columns for spectrum i.
For batman results, j is 0, and for batmanrerun results, j is 1.
batmanOptions.txt
The same file copied from batman input. This file will
be used by batmanrerun.
metabolitesList.txt
The same file copied from batman input.
NMRdata.txt
The same file copied from batman input.
If any plotting is performed, pdf files of the figure will be saved. For details,
please refer to each plotting functions.
batman documentation built on May 2, 2019, 6:13 p.m.
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description
batman and batmanrerun return the results as a data list with the objects described
in their individual function. They also put results in .txt format in a folder named
after the start execution time (date\_month\_hours\_mins\_seconds) within either folder ".../runBATMAN/BatmanOutput"
or folder "extdata" depending on batman input createDir settings.
Value
batman and batmanrerun save their results in the following files in the output folder:
beta_i_rr_j.txt |
A column vector (m \times 1) containing the estimated
posterior mean of relative concentrations for m fitted metabolites of spectrum i.
For |
beta_sam_i_rr_j.txt |
A matrix (m \times s) with each row containing the s posterior samples of
the relative concentrations for one fitted metabolite of spectrum i.
m is the total number of fitted metabolites. For |
delta_draw_mean_i.txt |
A column vector (M \times 1) containing the posterior mean of M multiplets ppm shift from the pre-set ppm position value in multi_data.csv or multi_data_user.csv of spectrum i. |
delta_sam_i.txt |
A matrix (s \times M) containing the posterior samples of M multiplets ppm shift. Every column correspond the shift posterior samples of one multiplet for spectrum i. M is the sum of all multiplets in the fitted metabolites. |
L_i.txt |
A matrix (t \times M) with each column as the template of one fitted metabolite for spectrum i before fitting. t is the number of data points in each spectrum. |
lambda_sam_i_rr_j.txt |
A column vector (s \times 1)
containing s posterior samples of λ (a scalar global precision
parameter) for spectrum i. For |
metabolitesListUsed.txt |
A column vector (m \times 1) containing the m metabolite names which have multiplets in/near the ppm region specified in batmanOptions.txt and used in the fitting. |
metaFit_sam_i_rr_j.txt |
A matrix (t \times s) containing
s posterior samples of total metabolites fit during MCMC iterations in
its columns for spectrum i. t is the number of data points in each spectrum.
For |
metaIndFit_sam_i_rr_j.txt |
A matrix (t \times (m*s))
containing s posterior samples of m individual metabolites fit in
its columns for spectrum i. t is the number of data points in each
spectrum. Every m columns are the m individual metabolite fit
samples for one posterior sample. For |
metaTemp_i_rr_j.txt |
A matrix t \times m) containing the posterior means of
m fitted metabolite templates in its columns (down sampled) after burn in
for spectra i. t is the number of data points in each spectrum.
For |
metaTempHR_i_rr_j.txt |
A matrix (t \times m) containing the posterior means of
m fitted metabolite templates in its columns (without down sample) after burn in
for spectra i. t is the number of data points (without down sample)
in each spectrum. For |
MultipletsPpmShifts.txt |
A table (M \times n) containing the posterior means of multiplets ppm shift for M multiplets as its rows. M is the sum of all multiplets in the fitted metabolites and n is the number of spectra analyzed. |
NMRdata_mod_i.txt |
A matrix (t \times 2) containing the input spectrum i in its original resolution. The first column is ppm value, and the second column is the ith spectrum intensity. |
RelCon.txt |
A table (m \times n) of the posterior means of relative concentrations for m fitted metabolites and n spectra. |
RelConCreInt.txt |
A table (m \times 2n) containing the 95% credible intervals (2.5% and 97.5%) for the relative concentrations of m fitted metabolites for n spectra. |
specFit_i_rr_j.txt |
A matrix (t \times 5) of BATMAN fit results with five columns as: [ppm, Original spectrum, Metabolites fit, Wavelet fit, Overall sum] of spectrum i.
For |
specFitHR_i_rr_j.txt |
A column vector (t \times 1) of
metabolite fit result in the original resolution for spectrum i. t is the
number of data points (without down sample) in each spectrum.
For |
theta_sam_i_rr_j.txt |
A matrix (t \times s) containing
s samples of wavelet fit during MCMC iterations in its columns for spectrum i.
For |
batmanOptions.txt |
The same file copied from batman input. This file will
be used by |
metabolitesList.txt |
The same file copied from batman input. |
NMRdata.txt |
The same file copied from batman input. |
If any plotting is performed, pdf files of the figure will be saved. For details, please refer to each plotting functions.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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