Introduction | Input data | Using lhCreateMAE based on MultiAssayExperiment as data container | Data analysis | Correlation method | Heuristic method | Comparison of Selected Gene Lists | References | Session info
Package: Lheuristic 1.5.0
Sanchez Pla Alex
Lheuristic: Detection of scatterplots with L-shaped pattern
The Lheuristic package identifies scatterpots that follow and L-shaped, negative distribution. It can be used to identify genes regulated by methylation by integration of an expression and a methylation array. The package uses two different methods to detect expression and methyaltion L- shapped scatterplots. The parameters can be changed to detect other scatterplot patterns.
Authors:
Lheuristic_1.5.0.tar.gz
Lheuristic_1.5.0.zip(r-4.7)Lheuristic_1.5.0.zip(r-4.6)Lheuristic_1.5.0.zip(r-4.5)
Lheuristic_1.5.0.tgz(r-4.6-any)Lheuristic_1.5.0.tgz(r-4.5-any)
Lheuristic_1.5.0.tar.gz(r-4.7-any)Lheuristic_1.5.0.tar.gz(r-4.6-any)
Lheuristic_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Lheuristic/json (API)
| # Install 'Lheuristic' in R: |
| install.packages('Lheuristic', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/aspresearch/lheuristic/issues
Datasets:
- TCGAexpression - Expression data matrix obtained from TCGA, TCGA-COAD dataset
- TCGAmethylation - Methylation data matrix obtained from TCGA, TCGA-COAD dataset
On BioConductor:Lheuristic-1.5.0(bioc 3.24)Lheuristic-1.4.0(bioc 3.23)
dnamethylationstatisticalmethodmethylationarrayl-shapedmethylation-expressionscatterplot-matrix
Last updated from:6f0f0ae984. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 193 | ||
| linux-devel-x86_64 | NOTE | 358 | ||
| source / vignettes | OK | 257 | ||
| linux-release-x86_64 | NOTE | 338 | ||
| macos-release-arm64 | NOTE | 254 | ||
| macos-oldrel-arm64 | NOTE | 151 | ||
| windows-devel | NOTE | 229 | ||
| windows-release | NOTE | 250 | ||
| windows-oldrel | NOTE | 279 | ||
| wasm-release | OK | 146 |
Exports:binScorecalcFreqscheckPairingcorrelationSelectionlhCreateMAEmatCorrsmessageTitlenumScoreplotGeneByNameplotGeneSelplotGenesMatscoreGenesMattoReqMat
Dependencies:abindbackportsbase64encBiobaseBiocBaseUtilsBiocGenericsbootbroombslibcachemcarcarDatacheckmatecliclustercolorspacecorrplotcowplotcpp11data.tableDelayedArrayDerivdigestdoBydplyrenergyevaluatefarverfastmapfontawesomeforecastforeignFormulafracdifffsgenericsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragslgtablehighrHmischtmlTablehtmltoolshtmlwidgetsIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynompurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownrpartrstatixrstudioapiS4ArraysS4VectorsS7sassscalesSeqinfoSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| binScore | binScore |
| calcFreqs | calcFreqs |
| checkPairing | checkPairing |
| correlationSelection: A vector correlation function calculator | correlationSelection |
| lhCreateMAE: Create a MultiAssayExperiment with Methylation and Expression Data | lhCreateMAE |
| A row-wise correlation function calculator | matCorrs |
| messageTitle | messageTitle |
| numScore | numScore |
| plotGeneByName | plotGeneByName |
| plotGeneSel | plotGeneSel |
| plotGenesMat | plotGenesMat |
| scoreGenesMat | scoreGenesMat |
| Expression data matrix obtained from TCGA, TCGA-COAD dataset | TCGAexpression |
| Methylation data matrix obtained from TCGA, TCGA-COAD dataset | TCGAmethylation |
| toReqMat | toReqMat |
