Package: ITALICS 2.67.0
Guillem Rigaill
ITALICS: ITALICS
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
Authors:
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ITALICS.pdf |ITALICS.html✨
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-2.67.0(bioc 3.21)ITALICS-2.66.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 months agofrom:ae94ff4a69. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-mac | WARNING | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | NOTE | Jan 28 2025 |
| R-4.4-mac | NOTE | Jan 28 2025 |
| R-4.3-win | NOTE | Jan 28 2025 |
| R-4.3-mac | NOTE | Jan 28 2025 |
Exports:addInfoanalyseCGHfromQuartetToSnpfromSnpToQuartetgetConfDatgetCorrectiongetEffetgetModelgetQuartetgetResidugetSnpInfoITALICSreadQuartetCopyNbtrainITALICS
Dependencies:abindaffxparseraffyioaskpassawsawsMethodsBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapffforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGLADgluegslhttrIRangesITALICSDataiteratorsjsonlitelatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeoligooligoClassesopensslpd.mapping50k.xba240pkgconfigplogrpreprocessCoreR6rlangRSQLiteS4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc
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 |