Package: padma 1.23.0
Andrea Rau
padma: Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.
Authors:
padma_1.23.0.tar.gz
padma_1.23.0.zip(r-4.7)padma_1.23.0.zip(r-4.6)padma_1.23.0.zip(r-4.5)
padma_1.23.0.tgz(r-4.6-any)padma_1.23.0.tgz(r-4.5-any)
padma_1.23.0.tar.gz(r-4.7-any)padma_1.23.0.tar.gz(r-4.6-any)
padma_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
padma/json (API)
NEWS
| # Install 'padma' in R: |
| install.packages('padma', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/andreamrau/padma/issues
- LUAD_subset - Subset of batch-corrected multi-omic TCGA data in lung adenocarcinoma
- mirtarbase - Curated miR-target interaction predictions from miRTarBase
- msigdb - MSigDB canonical pathways and corresponding gene lists
On BioConductor:padma-1.23.0(bioc 3.24)padma-1.22.0(bioc 3.23)
softwarestatisticalmethodprincipalcomponentgeneexpressionpathwaysrnaseqbiocartamethylseq
Last updated from:836ee71cb5. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 205 | ||
| linux-devel-x86_64 | OK | 348 | ||
| source / vignettes | OK | 264 | ||
| linux-release-x86_64 | OK | 315 | ||
| macos-release-arm64 | OK | 252 | ||
| macos-oldrel-arm64 | OK | 243 | ||
| windows-devel | OK | 236 | ||
| windows-release | OK | 267 | ||
| windows-oldrel | OK | 250 | ||
| wasm-release | OK | 174 |
Exports:factorMapimputed_genesMFA_resultsngenesomicsContribpadmapadmaRunpathway_gene_deviationpathway_nameremoved_genesshow
Dependencies:abindbackportsbase64encBiobaseBiocBaseUtilsBiocGenericsbootbroombslibcachemcarcarDatacliclustercolorspacecowplotcpp11crosstalkDelayedArrayDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluateFactoMineRfarverfastmapflashClustfontawesomeforecastFormulafracdifffsgenericsGenomicRangesggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetsIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewMultiAssayExperimentmvtnormnlmenloptrnnetnumDerivotelpbkrtestpillarpkgconfigpromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownS4ArraysS4VectorsS7sassscalesscatterplot3dSeqinfoSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot an MFA factor map for individuals or partial factor map based on padma analysis | factorMap |
| Subset of batch-corrected multi-omic TCGA data in lung adenocarcinoma | LUAD_subset |
| Curated miR-target interaction predictions from miRTarBase | mirtarbase |
| MSigDB canonical pathways and corresponding gene lists | msigdb |
| Plot the omics contribution per MFA axis and the overall weighted contribution | omicsContrib |
| Calculate individualized deviation scores from multi-omic data | padma padma,list-method padma,MultiAssayExperiment-method padma-methods |
| padmaResults object and constructor | padmaResults padmaResults-class |
| Calculate individualized deviation scores from multi-omic data | padmaRun |
| Accessors for a padmaResults object. | imputed_genes imputed_genes,padmaResults-method MFA_results MFA_results,padmaResults-method ngenes ngenes,padmaResults-method pathway_gene_deviation pathway_gene_deviation,padmaResults-method pathway_gene_deviation-method pathway_name pathway_name,padmaResults-method removed_genes removed_genes,padmaResults-method show show,padmaResults-method |
| Summarize results from padma | summary summary,padmaResults-method summary-methods |
