Overview | The ITALICS method | Normalization of Affymetrix GeneChip Human Mapping chips | Parameter tuning for ITALICS and sensitivity analysis to GLAD parameters | References
Package: ITALICS 2.73.0
Guillem Rigaill
ITALICS: ITALICS
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
Authors:
ITALICS_2.73.0.tar.gz
ITALICS_2.73.0.zip(r-4.7)ITALICS_2.73.0.zip(r-4.6)ITALICS_2.73.0.zip(r-4.5)
ITALICS_2.73.0.tgz(r-4.6-any)ITALICS_2.73.0.tgz(r-4.5-any)
ITALICS_2.73.0.tar.gz(r-4.7-any)ITALICS_2.73.0.tar.gz(r-4.6-any)
ITALICS_2.73.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ITALICS/json (API)
| # Install 'ITALICS' in R: |
| install.packages('ITALICS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:ITALICS-2.73.0(bioc 3.24)ITALICS-2.72.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:6fd5daf202. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 337 | ||
| linux-devel-x86_64 | NOTE | 436 | ||
| source / vignettes | OK | 349 | ||
| linux-release-x86_64 | NOTE | 406 | ||
| macos-release-arm64 | NOTE | 270 | ||
| macos-oldrel-arm64 | NOTE | 259 | ||
| windows-devel | NOTE | 303 | ||
| windows-release | NOTE | 296 | ||
| windows-oldrel | NOTE | 297 | ||
| wasm-release | OK | 260 |
Exports:addInfoanalyseCGHfromQuartetToSnpfromSnpToQuartetgetConfDatgetCorrectiongetEffetgetModelgetQuartetgetResidugetSnpInfoITALICSreadQuartetCopyNbtrainITALICS
Dependencies:abindaffxparseraffyioawsawsMethodsBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicodetoolscpp11crayonDBIDelayedArrayfastmapffforeachgenericsGenomicRangesGLADgluegslIRangesITALICSDataiteratorslatticelifecycleMatrixMatrixGenericsmatrixStatsmemoiseoligooligoClassespd.mapping50k.xba240pkgconfigpreprocessCorerlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| add info to quartet annotation | addInfo |
| GLAD analysis | analyseCGH |
| Compute the copy number of each SNP from its quartets intensities | fromQuartetToSnp |
| Function to get from snp to quartet | fromSnpToQuartet |
| Elimination of badly predicted probes | getConfDat |
| Correction | getCorrection |
| Effet | getEffet |
| Regression Model | getModel |
| Function to retrieve the information of each quartet | getQuartet |
| Correction | getResidu |
| Function to retrieve the chromosome and the position of each SNP on a given Affymetrix SNP array | getSnpInfo |
| Affymetrix SNP chip normalization | ITALICS Italics italics |
| Read PM probes of selected quartets and compute the quartet intensity | readQuartetCopyNb |
| ITALICS training | trainITALICS trainItalics trainitalics |