Fluxomics

C13ConfidenceInterval(v0, expdata, model, max_score, directions, majorIterationLimit)[source]
USAGE

[vs, output, v0] = C13ConfidenceInterval (v0, expdata, model, max_score, directions, majorIterationLimit)

INPUTS

  • v0 – set of flux vectors to be used as initial guesses. They may be valid or not.

  • expdata – experimental data

  • model – the standard model. Additional field .N (= null(S)) should also be provided. This is a basis of the flux space.

  • max_score – maximum allowable data fit error

OPTIONAL INPUTS

  • directions – ones and zeros of which reactions to compute (size = n x 1) or numbers of reactions to use aka. [1; 5; 7; 8; 200] or reaction strings aka. {‘GPK’, ‘PGL’}. Ratios are possible with this input only. Default = [] meaning - do FVA with no ratios.

  • majorIterationLimit – default = 10000

OUTPUT

  • vs – matrix

  • output – structure

  • v0 – as in input

compareBinsOfFluxes(xglc, model, sammin, sammax, metabolites)[source]

Takes the overall sammin and sammax samples, bins them into separate bin sizes and compares them, then compares the results to the largest bin size. calls [totalz, zscore, mdv1, mdv2] = compareTwoSamp(xglc, model, samp1, samp2, measuredMetabolites) sammin and sammax each contain bins of fluxes in x.samps(r,1).points

USAGE

[output] = compareBinsOfFluxes (xglc, model, sammin, sammax, metabolites)

INPUTS

  • xglc – sugar distribution

  • model – model structure

  • sammin – samples containing bins of fluxes

  • sammax – samples containing bins of fluxes

OPTIONAL INPUT

metabolites – list of metabolites

OUTPUT

output – result of comparison

compareMultSamp(xglc, model, samps, measuredMetabolites)[source]

Compare the multiple sets of samples

USAGE

[totalz, zscore, mdvs] = compareMultSamp (xglc, model, samps, measuredMetabolites)

INPUTS

  • xglc – sugar distribution, a random sugar distribution is calculated if empty

  • model – model structure, expects model.rxns to contain a list of rxn names

  • samps – samples, expects to have a field named points containing an array of sampled points

OPTIONAL INPUT

measuredMetabolites – parameter fed to calcMDVfromSamp.m which only calculates the MDVs for the metabolites listed in this array

OUTPUTS

  • totalz – sum of all zscores

  • zscore – calculated difference for each mdv element distributed across all the points

  • mdvs – contains fields:

    • mdv - the calculated mdv distribution converted from the idv solved from each point contained in their respective samples sampX

    • names - the names of the metabolites

    • ave - the average of each mdv element across all of the points

    • stdev - the standard dev for each mdv element across all points

compareTwoMDVs(mdv1, mdv2)[source]

Compares the 2 sets of mdvs

USAGE

[totalz, zscore] = compareTwoMDVs (mdv1, mdv2)

INPUT

mdv1, mdv2 – contains fields:

  • mdv - the calculated mdv distribution converted from the idv solved from each point contained in their respective samples sampX

  • names - the names of the metabolites

  • ave - the average of each mdv element across all of the points

  • stdev - the standard dev for each mdv element across all points

OUTPUTS

  • totalz – sum of all zscores

  • zscore – calculated difference for each mdv element distributed across all the points

compareTwoSamp(xglc, model, samp1, samp2, measuredMetabolites)[source]

Compare the 2 sets of samples

USAGE

[totalz, zscore, mdvs] = compareMultSamp (xglc, model, samps, measuredMetabolites)

INPUTS

  • xglc – sugar distribution, a random sugar distribution is calculated if empty

  • model – model structure, expects model.rxns to contain a list of rxn names

  • samp1, samp2 – samples, expects samp1 and samp2 to have a field named points containing an array of sampled points

OPTIONAL INPUT

measuredMetabolites – parameter fed to calcMDVfromSamp.m which only calculates the MDVs for the metabolites listed in this array

OUTPUTS

  • totalz – sum of all zscores

  • zscore – calculated difference for each mdv element distributed across all the points

  • mdv1, mdv2 – contains fields:

    • mdv - the calculated mdv distribution converted from the idv solved from each point contained in their respective samples sampX

    • names - the names of the metabolites

    • ave - the average of each mdv element across all of the points

    • stdev - the standard dev for each mdv element across all points

fitC13Data(v0, expdata, model, majorIterationLimit)[source]
USAGE

[vout, rout] = fitC13Data (v0, expdata, model, majorIterationLimit)

INPUTS

  • v0 – It will automatically be converted to alpha by solving N*alpha = v; if v0 is a matrix then it is assumed to be a multiple start situation and vout will also have this size.

  • expdata – either a data structure or a cell array of structures, in which case it is assumed that you wan to fit the sum of the scores

  • model – model structure

OPTIONAL INPUT

majorIterationLimit – max number of iterations solver is allowed to take. Default = 1000

OUTPUTS

  • vout – reflects size of v0, result of NLPsolution

  • rout – cell, result of NLPsolution

getBinsOfFluxes(samp, numfluxes, numbins)[source]

Takes a samp.points fluxes and bin them by numfluxes (remainder not used) or divide up in to bins of fluxes by numbins (remainder not used) sample each bin of fluxes and compare the differences between them.

USAGE

[output] = getBinsOfFluxes (samp, numfluxes, numbins)

INPUTS

  • samp – fluxes

  • numfluxes – default = 100

  • numbins – default = []

OUTPUT

output – structure with .samps field

getCompareBinsOfFluxes(xglc, model, samplo, samphi, metabolites)[source]

Compares the bins of fluxes between samplo and samphi, calls compareBinsOfFluxes(xglc, model, sammin, sammax, metabolites). `samplo and samphi each contain samples in x.points

USAGE

[output] = getCompareBinsOfFluxes (xglc, model, samplo, samphi, metabolites)

INPUTS

  • xglc – sugar distribution

  • model – model structure

  • samplo – samples containing bins of fluxes

  • samphi – samples containing bins of fluxes

OPTIONAL INPUT

metabolites – list of metabolites

OUTPUT

output – result of comparison

getRandGlc()[source]

Generates random glucose in isotopomer format

USAGE

[xGlc] = getRandGlc()

OUTPUT

xGlc – random glucose

goodInitialPoint(model, n)[source]

Generates 4*length(model.lb) random points, takes linear combinations of them so that all points are in the interior.

USAGE

[out] = goodInitialPoint (model, n)

INPUTS

  • model – model structure

  • n – number, default = 1

OUTPUT

out – random points with linear combinations

isotopomerViewer(mdv1, mdv2, names)[source]

Takes in an “experiment” and views the isotopomer as distributions between mdv1 and mdv2. No output.

USAGE

isotopomerViewer (mdv1, mdv2, names)

INPUTS

  • mdv1, mdv2 – structures

  • names – names in the plot

naturallabel(n)[source]

Returns a natural label idv of n carbons. Assumes 1.1% C13

USAGE

[out] = naturallabel (n)

INPUT

n – size of label

OUTPUT

out – natural label idv of n carbons

runHiLoExp(experiment)[source]

Takes an experiment with the following structure and splits the sample space at the median of a target flux solves the two spaces with a given sugar and compares the resulting mdvs to provide a z-score.

USAGE

[experiment] = runHiLoExp (experiment)

INPUTS

experiment – contains:

  • model with fields:

    • S = the stoichiometric matrix

    • rxns = array of reaction names, corresponding the S

    • c = optimization target 1, or -1

    • ub,lb = upper and lower bounds of reactions

  • points = a #fluxes X #samples (~2000) array of the solution space if missing or empty, will generate a sample

  • glcs = an array of sugars in isotopomer format, each column a separate sugar. Should not be in MDV format. Conversion is done automatically. will default to generate 1 random sugar if set to []

  • targets = an array of cells with string for the reaction to split on the solution space, defaults to ‘PGL’

  • thresholds = #targets X 1 array of thresholds

  • metabolites = an optional parameter fed to calcMDVfromSamp.m which only calculates the MDVs for the metabolites listed in this array. e.g - optionally, metabolites can also be a structure of fragments

  • hilo = a #targets X #samples array of 0/1’s, 0 id’s the sample of fluxes as the lo side and 1 id’s the sample for the hi side. hilo will only be calculated/recalculated if it’s missing or if the targets have been replaced using the param list

  • mdvs = structure of mdv results:

    • (name) = name of the run = t + glc# e.g. t1, t2, glc# refers to the glc in the glcs array.

score_KS(mdv, hilo, lambda)[source]

Calculates KS score

USAGE

[out] = score_ridge (mdv, hilo, lambda, crossval)

INPUTS

  • mdv – structure

  • hilo – (0’s and 1’s), ideally there will be a similar # of each.

OPTIONAL INPUTS

lambda – weighting, if the mean is less than lambda, the scores get weighted less, default = .02

OUTPUT

out – score

score_ridge(mdv, hilo, lambda, crossval)[source]

Calculates ridge score

USAGE

[out] = score_ridge (mdv, hilo, lambda, crossval)

INPUTS

  • mdv – structure

  • hilo – (0’s and 1’s), ideally there will be a similar # of each.

OPTIONAL INPUTS

  • lambda – ridge parameter, default = .01

  • crossval – whether to do cross validation. This severely slows down the computation, default is no.

OUTPUT

out – score