Package: altcdfenvs 2.75.0
Laurent Gautier
altcdfenvs: alternative CDF environments (aka probeset mappings)
Convenience data structures and functions to handle cdfenvs
Authors:
altcdfenvs_2.75.0.tar.gz
altcdfenvs_2.75.0.zip(r-4.7)altcdfenvs_2.75.0.zip(r-4.6)altcdfenvs_2.75.0.zip(r-4.5)
altcdfenvs_2.75.0.tgz(r-4.6-any)altcdfenvs_2.75.0.tgz(r-4.5-any)
altcdfenvs_2.75.0.tar.gz(r-4.7-any)altcdfenvs_2.75.0.tar.gz(r-4.6-any)
altcdfenvs_2.75.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
altcdfenvs/json (API)
| # Install 'altcdfenvs' in R: |
| install.packages('altcdfenvs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- cdfenvEx - CdfEnvAffy
On BioConductor:altcdfenvs-2.75.0(bioc 3.24)altcdfenvs-2.74.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarrayonechannelqualitycontrolpreprocessingannotationproprietaryplatformstranscription
Last updated from:9f56b80bdb. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 218 | ||
| linux-devel-x86_64 | NOTE | 257 | ||
| source / vignettes | OK | 345 | ||
| linux-release-x86_64 | NOTE | 258 | ||
| macos-release-arm64 | NOTE | 176 | ||
| macos-oldrel-arm64 | NOTE | 197 | ||
| windows-devel | NOTE | 555 | ||
| windows-release | NOTE | 468 | ||
| windows-oldrel | NOTE | 499 | ||
| wasm-release | OK | 172 |
Exports:appendCdfEnvAffybuildCdfEnv.biostringsbuildCdfEnv.matchprobescopyCdfEnvAffycountduplicatedcountskip.FASTA.entriesgeneNames.CdfEnvAffygetCdfEnvAffygetxy.probeseqgrep.FASTA.entryindex2xyindex2xy.CdfEnvAffyindexProbes.CdfEnvAffymatchAffyProbesmmProbesplot.CdfEnvAffyprint.FASTAprintValidCdfEnvAffyread.FASTA.entryread.n.FASTA.entriesread.n.FASTA.entries.splitread.n.FASTA.headersread.n.FASTA.sequencesremoveIndexskip.FASTA.entrytoHypergraphunique.CdfEnvAffyvalidAffyBatchvalidCdfEnvAffywrapCdfEnvAffywrite.FASTAxy2indexxy2index.CdfEnvAffy
Dependencies:affyaffyioBiobaseBiocGenericsBiocManagerBiostringscrayongenericsgraphhypergraphIRangesmakecdfenvpreprocessCoreS4VectorsSeqinfoXVector
altcdfenvs
Rendered fromaltcdfenvs.Rnwusingutils::Sweaveon May 29 2026.Last update: 2013-11-01
Started: 2013-11-01
Alternative CDF environments for 2(or more)-genomes chips
Rendered fromngenomeschips.Rnwusingutils::Sweaveon May 29 2026.Last update: 2019-02-25
Started: 2013-11-01
Modifying existing CDF environments to make alternative CDF environments
Rendered frommodify.Rnwusingutils::Sweaveon May 29 2026.Last update: 2019-02-25
Started: 2013-11-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class "AffyProbesMatch" | AffyProbesMatch-class combine,AffyProbesMatch,AffyProbesMatch-method show,AffyProbesMatch-method toHypergraph,AffyProbesMatch-method |
| append probe sets to a CdfEnvAffy | appendCdfEnvAffy |
| Build CDF environments | buildCdfEnv.biostrings |
| Class "CdfEnvAffy" | CdfEnvAffy-class coerce,CdfEnvAffy,Cdf-method coerce,CdfEnvAffy,environment-method geneNames,CdfEnvAffy-method index2xy,CdfEnvAffy-method indexProbes,CdfEnvAffy,character-method plot,CdfEnvAffy,missing-method show,CdfEnvAffy-method toHypergraph,CdfEnvAffy-method xy2index,CdfEnvAffy-method [,CdfEnvAffy,character,missing,missing-method |
| CdfEnvAffy | cdfenvEx |
| functions related to cdfenvs | buildCdfEnv.matchprobes CdfEnv getCdfEnvAffy wrapCdfEnvAffy |
| make a copy of a CdfEnvAffy | copyCdfEnvAffy |
| Count the number of times probes are used | countduplicated |
| get the names of the known probe sets | geneNames.CdfEnvAffy |
| A function to get the XY coordinates from a probes sequences data frame | getxy.probeseq |
| Functions to shuttle from indexes to XY coordinates | index2xy index2xy.CdfEnvAffy xy2index xy2index.CdfEnvAffy |
| indexes for probes | indexProbes.CdfEnvAffy |
| Match the probes on an Affymetrix array | matchAffyProbes mmProbes |
| A function to `plot' a CdfEnvAffy | plot.CdfEnvAffy |
| Functions to work with FASTA files / connections | countskip.FASTA.entries grep.FASTA.entry print.FASTA read.FASTA.entry read.n.FASTA.entries read.n.FASTA.entries.split read.n.FASTA.headers read.n.FASTA.sequences skip.FASTA.entry write.FASTA |
| A function to remove probes in an environment | removeIndex |
| Transform to an hypergraph | toHypergraph |
| Remove duplicated elements from a CdfEnvAffy | unique.CdfEnvAffy |
| Check validity of a CdfEnvAffy. | printValidCdfEnvAffy validAffyBatch validCdfEnvAffy |
