Package: omicRexposome 1.27.0

Xavier Escribà Montagut

omicRexposome: Exposome and omic data associatin and integration analysis

omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).

Authors:Carles Hernandez-Ferrer [aut, cre], Juan R. González [aut]

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omicRexposome.pdf |omicRexposome.html✨
omicRexposome/json (API)

# Install 'omicRexposome' in R:

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

Datasets:

asr - 'ResultSet' for testing and illustration purpouses
crs - 'ResultSet' for testing and illustration purpouses
mds - 'MultiDataSet' for testing and illustration purpouses

On BioConductor:omicRexposome-1.27.0(bioc 3.20)omicRexposome-1.26.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

11 exports 1.24 score 216 dependencies 2 mentions

Last updated 2 months agofrom:33b689f060

Exports:add_cls add_exp association crossomics getIntegration plotAssociation plotHits plotIntegration plotLambda tableHits tableLambda

Dependencies:abind ade4 annotate AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob boot broom bslib cachem calibrate car carData caTools checkmate circlize cli clipr clue cluster codetools colorspace corrplot cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray Deriv digest doBy dplyr DT edgeR ellipse emmeans estimability evaluate FactoMineR fansi farver fastICA fastmap flashClust fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel ggridges glmnet GlobalOptions glue gmm gplots gridExtra gtable gtools haven highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr impute imputeLCMD IRanges isoband isva iterators JADE jomo jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 lobstr locfit lsr made4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mice microbenchmark mime minqa mitml modelr multcompView MultiDataSet munsell mvtnorm nlme nloptr nnet norm numDeriv omicade4 openssl ordinal pan pbkrtest pcaMethods pillar pixmap pkgconfig plogr plyr PMA png prettyunits progress promises pryr purrr qqman quantreg qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen readr reshape2 rexposome rlang rmarkdown rpart RSpectra RSQLite rstudioapi S4Arrays S4Vectors sandwich sass scales scatterplot3d shape SmartSVA snow sp SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sva sys tibble tidyr tidyselect tinytex tmvtnorm tzdb ucminf UCSC.utils utf8 vctrs viridis viridisLite vroom withr xfun XML xtable XVector yaml zlibbioc zoo

Exposome Data Integration with Omic Data

Carles Hernandez-Ferer and Juan R. Gonzalez

Rendered fromexposome_omic_integration.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-02-12
Started: 2017-03-31

Help page	Topics
Method to add an ExposomeClust to a MultiDataSet	add_cls add_cls,MultiDataSet,ExposomeClust-method
Method to add an ExposomeSet to a MultiDataSet	add_exp add_exp,MultiDataSet,ExposomeSet-method
'ResultSet' for testing and illustration purpouses	asr
# -------------------------- Method to perform an association study between transcriptome and exposom	association association,MultiDataSet-method
Function to perform a Transcriptome-Wide Association Study	crossomics crossomics,MultiDataSet-method
'ResultSet' for testing and illustration purpouses	crs
Method to extrat integration-feature result from a ResultSet	getIntegration getIntegration,ResultSet-method
'MultiDataSet' for testing and illustration purpouses	mds
omicRexposome: Package for exposome and omic data associatin and integration	omicRexposome-package omicRexposome
Function to draw de result of an association study	plotAssociation plotAssociation,ResultSet-method
Plot number of hits per result in ResultSet	plotHits plotHits,ResultSet-method
Function to draw de result of an integration study	plotIntegration plotIntegration,ResultSet-method
Plot lambda score for all results in a ResultSet	plotLambda plotLambda,ResultSet-method
Transforms the discrete genotype from a 'snpSet' to a 'matrix' of a continuous variable.	snpToContinuous snpToContinuous,SnpSet-method
Counts the number of hits on the results stored in a ResultSet	tableHits tableHits,ResultSet-method
Compute a lambda score on the results stored in a ResultSet	tableLambda tableLambda,ResultSet-method

Package: omicRexposome 1.27.0

omicRexposome: Exposome and omic data associatin and integration analysis

Exposome Data Integration with Omic Data

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