Package: iNETgrate 1.11.0

Habil Zare

iNETgrate: Integrates DNA methylation data with gene expression in a single gene network

The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.

Authors:Isha Mehta [aut], Ghazal Ebrahimi [aut], Hanie Samimi [aut], Habil Zare [aut, cre]

iNETgrate_1.11.0.tar.gz
iNETgrate_1.11.0.zip(r-4.7)iNETgrate_1.11.0.zip(r-4.6)iNETgrate_1.11.0.zip(r-4.5)
iNETgrate_1.11.0.tgz(r-4.6-any)iNETgrate_1.11.0.tgz(r-4.5-any)
iNETgrate_1.11.0.tar.gz(r-4.7-any)iNETgrate_1.11.0.tar.gz(r-4.6-any)
iNETgrate_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iNETgrate/json (API)

# Install 'iNETgrate' in R:

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

Bug tracker:https://github.com/bioconductor/biocmanager/issues

Datasets:

toyCleanedAml - A subset of cleaned TCGA-LAML data
toyComputEloci - A subset of weighted DNA methylation profile of TCGA-LAML data
toyEigengenes - A subset of weighted average of gene expression present in each module
toyRawAml - A subset of TCGA-LAML data

On BioConductor:iNETgrate-1.11.0(bioc 3.24)iNETgrate-1.10.0(bioc 3.23)

geneexpression rnaseq dnamethylation networkinference network graphandnetwork biomedicalinformatics systemsbiology transcriptomics classification clustering dimensionreduction principalcomponent mrnamicroarray normalization geneprediction kegg survival core-services

6.30 score 76 stars 3 scripts 26 exports 283 dependencies

Last updated from:23a996a207. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	584
linux-devel-x86_64	OK	859
source / vignettes	OK	820
linux-release-x86_64	OK	1163
macos-release-arm64	OK	621
macos-oldrel-arm64	OK	712
windows-devel	OK	1050
windows-release	OK	1007
windows-oldrel	OK	1048
wasm-release	OK	466

Exports:accelFailAnalysis analyzeSurvival bestInetgrator cleanAllData computEigengenes computEigenloci computeInetgrator computeUnion coxAnalysis createLocusGene distanceToTss electGenes filterLowCor findAliveCutoff findCore findTcgaDuplicates iNETgrate inferEigengenes makeNetwork plotKM plotLociNum plotLociTss prepareSurvival preprocessDnam sample2pat sampleData

Dependencies:abind aisdk annotate AnnotationDbi ape aplot askpass backports base64 base64enc beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocStyle Biostrings bit bit64 bitops blob bnlearn bookdown bslib bumphunter C50 cachem callr caret caTools checkmate cigarillo class cli clipr clock cluster clusterProfiler codetools colorspace cpp11 crayon Cubist curl data.table DBI dbplyr DelayedArray DelayedMatrixStats diagram digest dir.expiry doParallel doRNG DOSE dplyr dynamicTreeCut e1071 enrichit enrichplot evaluate farver fastcluster fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver foreach foreign formatR Formula fs futile.logger futile.options future future.apply gdata gdtools genefilter generics GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree glmnet globals glue GO.db GOSemSim gower gplots graph graphite graphlayouts gridExtra gridGraphics gson gtable gtools h5mread hardhat HDF5Array highr Hmisc hms Homo.sapiens htmlTable htmltools htmlwidgets httr httr2 igraph illuminaio impute inum ipred IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lava lazyeval libcoin lifecycle limma listenv locfit lubridate magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi ModelMetrics multtest mvtnorm nlme nnet nor1mix numDeriv openssl openxlsx org.Hs.eg.db OrganismDbi otel parallelly partykit patchwork pheatmap Pigengene pillar pkgconfig plyr png polyclip preprocessCore prettyunits pROC processx prodlim progress progressr proxy ps purrr quadprog qvalue R.methodsS3 R.oo R.utils R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel RCurl reactome.db ReactomePA readr recipes rentrez reshape reshape2 restfulr Rfast Rgraphviz rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer rvest S4Arrays S4Vectors S7 sass scales scatterpie scrime selectr Seqinfo shape siggenes snow SparseArray sparseMatrixStats sparsevctrs SQUAREM statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidydr tidygraph tidyr tidyselect tidytree timechange timeDate tinytex treeio tweenr TxDb.Hsapiens.UCSC.hg19.knownGene tzdb utf8 vctrs viridis viridisLite vroom WGCNA withr xfun XML xml2 xtable XVector yaml yulab.utils zigg zip

iNETgrate: Integrating gene expression and DNA methylation data in a gene network

1 Introduction | 2 How to run iNETgrate ? | 3 Session Information

Rendered fromiNETgrate_inference.Rnwusingknitr::knitr

Last update: 2023-06-27
Started: 2023-03-24

Help page	Topics
Integrates DNA methylation data with gene expression in a single gene network	iNETgrate-package
Accelerated Failure Analysis	accelFailAnalysis
Survival analysis	analyzeSurvival
Identifies the bestInetgrator	bestInetgrator
Cleans and preprocesses data	cleanAllData
Compute eigengenes of combined modules.	computEigengenes computEigengloci rename
Computes an eigenloci for each gene	computEigenloci
Computes an inetgrator	computeInetgrator
Computes union gene set	computeUnion
Cox analysis	coxAnalysis
Mapping one locus to one gene.	createLocusGene
Computes distance of loci to the closest TSS	distanceToTss
Download and save TCGA data	downloaData
Selects input genes for iNETgrate analysis.	electGenes
Filters out genes or loci	filterLowCor
Find Alive Cutoff	findAliveCutoff
Finds the most connected cluster of points	findCore
Identify and remove duplicate samples	findTcgaDuplicates
iNETgrate - Runs entire iNETgrate pipeline.	iNETgrate
Infers features for the test(validation) dataset	inferEigengenes
Make network	makeNetwork
Survival (Kaplan-Meier estimator) plots	plotKM
Plot number of loci per gene.	plotLociNum
Plots distance of loci to genes	plotLociTss
Prepare survival data	prepareSurvival
Cleans DNA methylation data	preprocessDnam
Maps sample IDs to corresponding patient IDs	sample2pat
Sample Data	sampleData
A subset of cleaned TCGA-LAML data	toyCleanedAml
A subset of weighted DNA methylation profile of TCGA-LAML data	toyComputEloci
A subset of weighted average of gene expression present in each module	toyEigengenes
A subset of TCGA-LAML data	toyRawAml

Package: iNETgrate 1.11.0

iNETgrate: Integrates DNA methylation data with gene expression in a single gene network

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