Package: RCM 1.23.0

Stijn Hawinkel

RCM: Fit row-column association models with the negative binomial distribution for the microbiome

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

Authors:Stijn Hawinkel [cre, aut]

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RCM.pdf |RCM.html✨
RCM/json (API)
NEWS

# Install 'RCM' in R:

install.packages('RCM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/centerforstatistics-ugent/rcm/issues

Datasets:

Zeller - Microbiomes of colorectal cancer patients and healthy controls

On BioConductor:RCM-1.23.0(bioc 3.21)RCM-1.22.0(bioc 3.20)

metagenomics dimensionreduction microbiome visualization ordination phyloseq rcm

6.90 score 16 stars 25 scripts 149 downloads 15 mentions 10 exports 90 dependencies

Last updated 2 months agofrom:0cde287bc5. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win	NOTE	Dec 18 2024
R-4.5-linux	NOTE	Dec 18 2024
R-4.4-win	NOTE	Dec 18 2024
R-4.4-mac	NOTE	Dec 18 2024
R-4.3-win	NOTE	Dec 18 2024
R-4.3-mac	NOTE	Dec 18 2024

Exports:addOrthProjection checkAlias extractCoord getDevianceRes inertia liks plotRespFun RCM RCM_NB residualPlot

Dependencies:ade4 alabama ape askpass Biobase BiocGenerics biomformat Biostrings cli cluster codetools colorspace cpp11 crayon curl data.table DBI digest edgeR fansi farver foreach generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable httr igraph IRanges isoband iterators jsonlite labeling lattice lifecycle limma locfit magrittr MASS Matrix mgcv mime multtest munsell nleqslv nlme numDeriv openssl permute phyloseq pillar pixmap pkgconfig plyr quadprog quantmod R6 RColorBrewer Rcpp RcppArmadillo reshape2 rhdf5 rhdf5filters Rhdf5lib rlang S4Vectors scales sp statmod stringi stringr survival sys tensor tibble tseries TTR UCSC.utils utf8 vctrs vegan VGAM viridisLite withr xts XVector zlibbioc zoo

Manual for the RCM pacakage

Rendered fromRCMvignette.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2021-10-26
Started: 2017-12-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
This function adds orthogonal projections to a given plot	addOrthProjection
An auxiliary R function to 'array' multiply an array with a vector, kindly provided by Joris Meys	arrayprod
A function to build a centering matrix based on a dataframe	buildCentMat
A function to build the confounder matrices	buildConfMat
buildConfMat.character	buildConfMat.character
buildConfMat.data.frame	buildConfMat.data.frame
A function to build the covariate matrix of the constraints	buildCovMat
A function to build the design matrix	buildDesign
Check for alias structures in a dataframe, and throw an error when one is found	checkAlias
Constrained correspondence analysis with adapted powers	constrCorresp
Replace missing entries in X by their expectation to set their contribution to the estimating equations to zero	correctXMissingness
A function to extract deviances for all dimension, including after filtering on confounders	deviances
A function that returns the value of the partial derivative of the log-likelihood ratio to alpha, keeping the response functions fixed	dLR_nb
A score function for the column components of the independence model (mean relative abundances)	dNBabundsOld
A score function for the row components of the independence model (library sizes)	dNBlibSizes
The score function of the response function for 1 taxon at the time	dNBllcol_constr
The score function of the general response function	dNBllcol_constr_noLab
Estimation of the parameters of a third degree GLM	dNBllcolNP
A score function for the estimation of the column scores in an unconstrained RC(M) model	dNBllcolOld
A score function of the NB for the row scores	dNBllrow
A score function for the psi of a given dimension	dNBpsis
A function that returns the coordinates of an ellipse	ellipseCoord
Estimate the overdispersion	estDisp
A function to estimate the taxon-wise NB-params	estNBparams
A function to estimate the NB-params ignoring the taxon labels	estNBparamsNoLab
Estimate the taxon-wise response functions non-parametrically	estNPresp
A function to extract plotting coordinates, either for plot.RCM or to export to other plotting software	extractCoord
A function to extract a matrix of expected values for any dimension of the fit	extractE
Filters out the effect of known confounders. This is done by fitting interactions of every taxon with the levels of the confounders. It returns a modified offset matrix for the remainder of the fitting procedure.	filterConfounders
A function to calculate the matrix of deviance residuals.	getDevianceRes
ACalculate the matrix of deviance residuals	getDevMat
A function to extract the influence for a given parameter index	getInflCol
Extract the influence of all observations on a given row score	getInflRow
Integrate the spline of an vgam object	getInt
Extract the logged likelihood of every count	getLogLik
A function to construct a model matrix of a certain degree	getModelMat
Return a matrix of row scores	getRowMat
Gram-Schmidt orthogonalization of vectors	GramSchmidt
Define linear equality constraints for env. gradient	heq_nb
The jacobian of the linear equality constraints	heq_nb_jac
Functions to indent the plot to include the entire labels	indentPlot
Calculate the log-likelihoods of all possible models	inertia
Jacobian of the constrained analysis with linear response function.	JacCol_constr
The jacobian of the response function without taxon labels	JacCol_constr_noLab
Calculate the log-likelihoods of all possible models	liks
Get the value of the log-likelihood ratio of alpha	LR_nb
A function that returns the Jacobian of the likelihood ratio	LR_nb_Jac
Calculate the components of the influence functions	NBalphaInfl
The influence function for the column scores	NBcolInfl
Jacobian for the column components of the independence model	NBjacobianAbundsOld
Jacobian function for the estimation of a third degree GLM	NBjacobianColNP
Jacobian for the estimation of the column scores	NBjacobianColOld
Jacobian for the raw components of the independence model	NBjacobianLibSizes
Jacobian for the psi of a given dimension	NBjacobianPsi
A jacobian function of the NB for the row scores	NBjacobianRow
The influence function for the psis	NBpsiInfl
The influence function for the row scores	NBrowInfl
Plot RC(M) ordination result with the help of ggplot2	plot.RCM
Plot the non-parametric response functions	plotRespFun
Wrapper function for the RCM() function	RCM RCM,matrix-method RCM,phyloseq-method
Fit the RC(M) model with the negative binomial distribution.	RCM_NB
Make residual plots	residualPlot
Calculates the Jacobian of the parametric response functions	respFunJacMat
Derivative of the Lagrangian of the parametric response function	respFunScoreMat
A function to efficiently row multiply a matrix and a vector	rowMultiply
A small auxiliary function for the length of the lambdas	seq_k
Trim based on confounders to avoid taxa with only zero counts	trimOnConfounders
Microbiomes of colorectal cancer patients and healthy controls	Zeller