Installation | Dependencies | Usage | Examples | print(mtx2$x.mod) | print(mtx2$mx.offset) | print(mtx2$mx.scale)
Package: MBQN 2.25.0
Eva Brombacher
MBQN: Mean/Median-balanced quantile normalization
Modified quantile normalization for omics or other matrix-like data distorted in location and scale.
Authors:
MBQN_2.25.0.tar.gz
MBQN_2.25.0.zip(r-4.7)MBQN_2.25.0.zip(r-4.6)MBQN_2.25.0.zip(r-4.5)
MBQN_2.25.0.tgz(r-4.6-any)MBQN_2.25.0.tgz(r-4.5-any)
MBQN_2.25.0.tar.gz(r-4.7-any)MBQN_2.25.0.tar.gz(r-4.6-any)
MBQN_2.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MBQN/json (API)
| # Install 'MBQN' in R: |
| install.packages('MBQN', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/arianeschad/mbqn/issues
On BioConductor:MBQN-2.25.0(bioc 3.24)MBQN-2.24.0(bioc 3.23)
normalizationpreprocessingproteomicssoftware
Last updated from:129a7b1e14. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 193 | ||
| linux-devel-x86_64 | NOTE | 201 | ||
| source / vignettes | OK | 159 | ||
| linux-release-x86_64 | NOTE | 187 | ||
| macos-release-arm64 | NOTE | 111 | ||
| macos-oldrel-arm64 | NOTE | 90 | ||
| windows-devel | NOTE | 88 | ||
| windows-release | NOTE | 96 | ||
| windows-oldrel | NOTE | 76 | ||
| wasm-release | OK | 124 |
Exports:getKminmaxgetPvaluembqnmbqnBoxplotmbqnGetIntersectmbqnGetNRIfeaturesmbqnGetThresholdmbqnNRImbqnPlotAllmbqnPlotRImbqnSimuDatambqnSimuDistortiononeSidedTesttruncateDecimals
Dependencies:abindaskpassbase64encBiobaseBiocFileCacheBiocGenericsbitbit64bitopsblobbslibcachemclassclicpp11curlDBIdbplyrDelayedArraydigestdplyre1071evaluatefarverfastmapfilelockfontawesomefsgenericsGenomicRangesggplot2gldgluegtablehighrhtmltoolshttr2IRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclelimmalmommagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormopensslPairedDatapillarpkgconfigpreprocessCoreproxypurrrR6rappdirsRColorBrewerRCurlrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Missing value pattern dataset | example_NApattern |
| Get the k largest/smallest elements | getKminmax |
| Calculates Pitman-Morgan variance test on two matrices | getPvalue |
| Mean/Median-balanced quantile normalization | mbqn |
| Combined box plot and line plot | mbqnBoxplot |
| Helper function for mbqnGetThreshold | mbqnGetIntersect |
| Identify rank invariant (RI) and nearly rank invariant (NRI) features | mbqnGetNRIfeatures |
| Calculates the rank invariance threshold from which on MBQN should be used instead of 'classical' QN | mbqnGetThreshold |
| Selective mean/median-balanced quantile normalization | mbqnNRI |
| Plot RI/NRI feature frequencies and normalized/unnormalized features | mbqnPlotAll |
| Plot frequency of detected RI/NRI features | mbqnPlotRI |
| Generate a random/structured data matrix | mbqnSimuData |
| Perturbation of sample mean and scale | mbqnSimuDistortion |
| Recalulate p value from two-sided to one-sided | oneSidedTest |
| Truncate float to defined number of decimal values | truncateDecimals |
