Package: MOSClip 1.1.0

Paolo Martini

MOSClip: Multi Omics Survival Clip

Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.

Authors:Paolo Martini [aut, cre], Anna Bortolato [aut], Anna Tanada [aut], Enrica Calura [aut], Stefania Pirrotta [aut], Federico Agostinis [aut]

MOSClip_1.1.0.tar.gz
MOSClip_1.1.0.zip(r-4.5)MOSClip_1.1.0.zip(r-4.4)
MOSClip_1.1.0.tgz(r-4.4-any)
MOSClip_1.1.0.tar.gz(r-4.5-noble)MOSClip_1.1.0.tar.gz(r-4.4-noble)
MOSClip_1.1.0.tgz(r-4.4-emscripten)
MOSClip.pdf |MOSClip.html✨
MOSClip/json (API)
NEWS

# Install 'MOSClip' in R:

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

Bug tracker:https://github.com/caluralab/mosclip/issues

Datasets:

multiOmics - Omics class object with TCGA ovarian data
multiOmicsTopo - Omics class object with TCGA ovarian data for topological analysis
ovarianDataset - ExperimentList class object with TCGA ovarian data
reactSmall - PathwayList of pathways from Reactome

On BioConductor:MOSClip-0.99.5(bioc 3.20)

software statisticalmethod graphandnetwork survival regression dimensionreduction pathways reactome

5.22 score 5 scripts 33 exports 206 dependencies

Last updated 2 days agofrom:412bda8a84. Checks:OK: 3 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024

Exports:addResamplingCounts annotePathwayToFather availableOmicMethods computeFreqs computeOmicsIntersections downloadPathwayRelationFromReactome getPathwaysModulesSuccess makeOmics multiOmicsSurvivalModuleTest multiOmicsSurvivalPathwayTest multiOmicsTwoClassModuleTest multiOmicsTwoClassPathwayTest multiPathwayModuleReport multiPathwayReport plotFrequencies plotModuleHeat plotModuleInGraph plotModuleKM plotModuleReport plotMultiPathwayReport plotPathwayHeat plotPathwayKM resamplingModulesSurvival resamplingModulesTwoClass resamplingPathwaySurvival resamplingPathwayTwoClass runSupertest selectStablePathwaysModules showModule showMOSpalette showOmics showPathway stripModulesFromPathways

Dependencies:abind annotate AnnotationDbi askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot broom bslib cachem car carData checkmate circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap corpcor corrplot cowplot coxrobust cpp11 crayon crosstalk curl data.table DBI DelayedArray Deriv digest doBy doParallel dplyr DT elasticnet ellipse emmeans estimability evaluate exactRankTests FactoMineR fansi farver fastmap flashClust fontawesome foreach formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtext GlobalOptions glue graph graphite gRbase gridExtra gridGraphics gridtext gtable highr htmltools htmlwidgets httpuv httr igraph IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST km.ci KMsurv knitr labeling lambda.r lars later lattice lazyeval leaps lifecycle lme4 magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat memoise mgcv microbenchmark mime minqa modelr multcompView MultiAssayExperiment munsell mvtnorm NbClust nlme nloptr nnet numDeriv openssl org.Hs.eg.db pbkrtest pheatmap pillar pkgconfig plogr plyr png polynom promises purrr qpgraph qtl quantreg R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape restfulr Rgraphviz Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rstatix rtracklayer S4Arrays S4Vectors sass scales scatterplot3d shape snow SparseArray SparseM stringi stringr SummarizedExperiment SuperExactTest survival survminer survMisc sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XML xml2 xtable XVector yaml yulab.utils zlibbioc zoo

MOSClip vignette

Rendered frommosclip_vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-15
Started: 2024-09-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Find Pathway Fathers	annotePathwayToFather
Get available Omics Summarizing Methods	availableOmicMethods
Check if all the list object have the same order of pathway module	checkOrder filterExpr filterMultiOmicsForSamples mergeCol preparePerms resolveAndOrder
Regular PCA	compPCs
Compute Frequencies in a Named List	computeFreqs
Compute Omics Intersections	computeOmicsIntersections
compute PCs.	computePCs
A generic function to convert pathway	convertPathway
Create Cox Object	createCoxObj
Create Data Module	createDataModule
Create the list of covariates that are going to be tested	createMOMView
Download Reactome Pathway Relations	downloadPathwayRelationFromReactome
Estimate Single Covariance Matrix	estimateExprCov
Extract the maximal cliques	extractCliquesFromDag mmmoralize
Extract Summary Binary from MultiOmics Objects	extractSummaryFromBinary
Extract Summary Cluster from MultiOmics Objects	extractSummaryFromCluster
Extract Summary Binary from MultiOmics Objects	extractSummaryFromNumberOfEvents
Extract Summary PCA from MultiOmics Objects	extractSummaryFromPCA
Retrieves pathways relatives	getPathFathers
Two-classes glm test.	glmTest
Guess the most influent features from MultiOmics Survival or Two-class results.	guessInvolvement
Guess the most influent features from MultiOmics Survival or Two-class results.	guessInvolvementPathway
Convert id to pathway name	id2name
Omics class initializer function	makeOmics
Make positive and definite covariance matrix	makePositiveDefinite
Map Pathways ID from Graphite	mapPathwaysIDfromGraphite
Minimum or NA	minOrNA
MOSClip: Multi-Omics Survival Clip	MOSClip-package MOSClip
Omics class object with TCGA ovarian data	multiOmics
Multi Omics Modules.	MultiOmicsModules-class showModule,MultiOmicsModules-method
Multi Omics Pathway.	MultiOmicsPathway-class showPathway,MultiOmicsPathway-method
Compute Multi Omics Survival in Pathway Modules	multiOmicsSurvivalModuleTest
Compute Multi Omics Survival in Pathways	multiOmicsSurvivalPathwayTest
Omics class object with TCGA ovarian data for topological analysis	multiOmicsTopo
Computes Multi Omics Two-Class in Pathway Modules	multiOmicsTwoClassModuleTest
Compute Multi Omics Two-Class in Pathways	multiOmicsTwoClassPathwayTest
Provides a Table of the Modules Test Results	multiPathwayModuleReport
Summarize pathways' info from a list of MultiOmicsPathway objects (MOP)	multiPathwayReport
Omics.	Omics Omics-class showOmics,Omics-method
ExperimentList class object with TCGA ovarian data	ovarianDataset
Plot Frequencies of Pathway Fathers for Omics intersection	plotFrequencies
Plot a Heatmap of a Module by Omics	plotModuleHeat
Plot a Directed Graph of the MultiOmicsModules Object	plotModuleInGraph
Plot Kaplan-Meier survival curves of a specific module	plotModuleKM
Plot a table of a 'MultiOmicsModules' (MOM) object	plotModuleReport
Summarize and plot pathways' info from a list of 'MultiOmicsPathway' (MOP)	plotMultiPathwayReport
Plot heatmaps of the pathway by omics	plotPathwayHeat
Plot Kaplan-Meier survival curves of a specific pathway	plotPathwayKM
Compute pvalue Summary	pvalueSummary
PathwayList of pathways from Reactome	reactSmall
Remove self loops from a graphNEL	removeSelfLoops
Resampling function for survival analysis on modules	resamplingModulesSurvival resamplingPathwaySurvival
Resampling function for two-class analysis on modules	resamplingModulesTwoClass resamplingPathwayTwoClass
Performs a Exact test - analysis of omics intersection	runSupertest
Select stable pathway modules	addResamplingCounts getPathwaysModulesSuccess selectStablePathwaysModules
A generic function showing pathway's module info	showModule
Shows the MOSClip palette.	showMOSpalette
A generic functions showing parameter associated with each omics	showOmics
A generic function showing pathway info	showPathway
Sparse PCA	sparseCompPCs
Remove Module Number From Pathway Name	stripModulesFromPathways
Summarize Using Cluster Analysis	summarizeInCluster
Summarize Omics Covaraites By Min Pvalue	summarizeOmicsResByMinPvalue
Summarize To Binary Directional Events	summarizeToBinaryDirectionalEvents
Summarize To Binary Events	summarizeToBinaryEvents
Summarize With Directed Sum	summarizeToNumberOfDirectionalEvents
Summarize To Number of Binary Events	summarizeToNumberOfEvents
Summarize Using PCA	summarizeWithPca
Cox Model Analysis	survivalcox
Cox Robust Model Analysis	coxrsummary survivalcoxr
Topological PCA	topoCompPCs