# Compositional omics model based visual integration

## Documentation for package ‘combi’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

addLink | Add a link on a compositional plot
arrayMult | Array multiplication
buildCentMat | A function to build a centering matrix based on a dataframe
buildCompMat | Build the composition matrix for a certain dimension m dimensions
buildConfMat | Build confounder design matrices with and without intercepts
buildCovMat | A function to build the covariate matrix of the constraints
buildEmptyJac | Prepare an empty Jacobian matrix, with useful entries prefilled. In case of distribution "gaussian", it returns the lhs matrix of the linear system for finding the feature paramters
buildMarginalOffset | Build an offset matrix from an marginal model object
buildMu | A function to build the mu matrix
buildMuMargins | Build the marginal mu matrix
buildOffsetModel | Build a marginal offset matrix given a model
checkAlias | Check for alias structures in a dataframe, and throw an error when one is found
checkMeanVarTrend | Quickly check if the mean variance trend provides a good fit
checkMonotonicity | Check for monotonicity in compositional datasets fro given dimensions
combi | Perform model-based data integration
convPlot | Plot the convegrence of the different parameter estimates in a line plot
deriv2LagrangianFeatures | The score function to estimate the latent variables
deriv2LagrangianLatentVars | The jacobian function to estimate the latent variables
deriv2LagrangianLatentVarsConstr | The score function to estimate the latent variables
derivLagrangianFeatures | The score function to estimate the feature parameters
derivLagrangianLatentVars | The score function to estimate the latent variables
derivLagrangianLatentVarsConstr | The score function to estimate the latent variables
estFeatureParameters | Estimate the feature parameters
estIndepModel | Estimate the independence model belonging to one view
estLatentVars | Estimate the latent variables
estMeanVarTrend | Estimate a column-wise mean-variance trend
estOff | Estimate the row/column parameters of the independence model
extractCoords | Extract coordinates from fitted object
extractData | Helper function to extract data matrix from phyloseq, expressionset objects etc. Also filers out all zero rows
extractMat | A function to extract a data matrix from a number of objects
extractMat-method | A function to extract a data matrix from a number of objects
filterConfounders | Filter out the effect of known confounders
getInflLatentVar | Extract the influence on the estimation of the latent variable
gramSchmidtOrth | Gram schimdt orhtogonalize a with respect to b, and normalize
indentPlot | Functions to indent the plot to include the entire labels
inflPlot | A ggplot line plot showing the influences
influence.combi | Evaluate the influence function
jacConfounders | Jacobian when estimating confounder variables
jacConfoundersComp | Jacobian for conditioning under compositionality
jacFeatures | Evaluate the jacobian for estimating the feature parameters for one view
jacLatentVars | Evaluate the jacobian for estimating the latent variable for one view
jacLatentVarsConstr | Evaluate the jacobian for estimating the latent variable for one view for constrained ordination
plot.combi | Make multiplots of the data integration object
polyHorner | Horner's method to evaluate a polynomial, copied from the polynom package. the most efficient way
predictSpline | A custom spline prediction function, extending linearly with a slope such that prediction never drops below first bisectant
prepareJacMat | prepare the jacobian matrix
prepareJacMatComp | prepare the jacobian for the latent variabels compostional
prepareScoreMat | Prepare a helper matrix for score function evaluation under quasi-likelihood
print.combi | Print an overview of a fitted combi x
quasiJacIndep | The jacobian for column offset estimation
quasiScoreIndep | Quasi score equations for column offset parameters of sequence count data
rowMultiply | A function to efficiently row multiply a matrix and a vector
scaleCoords | A helper function to rescale coordinates
scoreConfounders | Score functions for confounder variables
scoreConfoundersComp | Score equations for conditioning under compositionality
scoreFeatureParams | Evaluate the score functions for the estimation of the feature parameters for a single dataset
scoreLatentVars | Evaluate the score functions for the estimation of the latent variables for a single dataset
seqM | A small auxiliary function for the indices of the lagrange multipliers
trimOnConfounders | Trim based on confounders to avoid taxa with only zero counts
zhangMetabo | Metabolomes of mice that underwent Pulsed Antibiotic Treatment (PAT) and controls
zhangMetavars | Baseline sample variables of PAT and control mice
zhangMicrobio | Microbiomes of mice that underwent Pulsed Antibiotic Treatment (PAT) and controls