Package: ITALICS 2.65.0
Guillem Rigaill
ITALICS: ITALICS
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
Authors:
ITALICS_2.65.0.tar.gz
ITALICS_2.65.0.zip(r-4.5)ITALICS_2.65.0.zip(r-4.4)ITALICS_2.65.0.zip(r-4.3)
ITALICS_2.65.0.tgz(r-4.4-any)ITALICS_2.65.0.tgz(r-4.3-any)
ITALICS_2.65.0.tar.gz(r-4.5-noble)ITALICS_2.65.0.tar.gz(r-4.4-noble)
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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-2.65.0(bioc 3.20)ITALICS-2.64.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:aa5345938f
Exports:addInfoanalyseCGHfromQuartetToSnpfromSnpToQuartetgetConfDatgetCorrectiongetEffetgetModelgetQuartetgetResidugetSnpInfoITALICSreadQuartetCopyNbtrainITALICS
Dependencies:abindaffxparseraffyioaskpassawsawsMethodsBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapffforeachGenomeInfoDbGenomeInfoDbDataGenomicRangesGLADgluegslhttrIRangesITALICSDataiteratorsjsonlitelatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeoligooligoClassesopensslpd.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 |