altcdfenvs: alternative CDF environments (aka probeset mappings)

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Convenience data structures and functions to handle cdfenvs

Author
Laurent Gautier <lgautier@gmail.com>
Date of publication
None
Maintainer
Laurent Gautier <lgautier@gmail.com>
License
GPL (>= 2)
Version
2.36.0

View on Bioconductor

Man pages

AffyProbesMatch-class
Class "AffyProbesMatch"
appendCdfEnvAffy
append probe sets to a CdfEnvAffy
buildCdfEnv.biostrings
Build CDF environments
cdfenv
functions related to cdfenvs
CdfEnvAffy-class
Class "CdfEnvAffy"
cdfenvEx
CdfEnvAffy
copyCdfEnvAffy
make a copy of a CdfEnvAffy
countduplicated
Count the number of times probes are used
geneNames
get the names of the known probe sets
getxy.probeseq
A function to get the XY coordinates from a probes sequences...
index2xy
Functions to shuttle from indexes to XY coordinates
indexProbes.CdfEnvAffy
indexes for probes
matchAffyProbes
Match the probes on an Affymetrix array
plot.CdfEnvAffy
A function to 'plot' a CdfEnvAffy
removeIndex
A function to remove probes in an environment
toHypergraph
Transform to an hypergraph
unique.CdfEnvAffy
Remove duplicated elements from a CdfEnvAffy
utils.FASTA
Functions to work with FASTA files / connections
validAffyBatch
Check validity of a CdfEnvAffy.

Files in this package

altcdfenvs/DESCRIPTION
altcdfenvs/NAMESPACE
altcdfenvs/R
altcdfenvs/R/CdfEnv.R
altcdfenvs/R/appendCdfEnvAffy.R
altcdfenvs/R/buildCdfEnv.biostrings.R
altcdfenvs/R/buildCdfEnv.matchprobes.R
altcdfenvs/R/cdfenvs.R
altcdfenvs/R/copyCdfEnvAffy.R
altcdfenvs/R/readFASTA.R
altcdfenvs/R/removeIndex.R
altcdfenvs/R/unique.CdfEnvAffy.R
altcdfenvs/build
altcdfenvs/build/vignette.rds
altcdfenvs/data
altcdfenvs/data/cdfenvEx.rda
altcdfenvs/inst
altcdfenvs/inst/CITATION
altcdfenvs/inst/UnitTests
altcdfenvs/inst/UnitTests/AffyProbesMatch_test.R
altcdfenvs/inst/doc
altcdfenvs/inst/doc/altcdfenvs.R
altcdfenvs/inst/doc/altcdfenvs.Rnw
altcdfenvs/inst/doc/altcdfenvs.pdf
altcdfenvs/inst/doc/modify.R
altcdfenvs/inst/doc/modify.Rnw
altcdfenvs/inst/doc/modify.pdf
altcdfenvs/inst/doc/ngenomeschips.R
altcdfenvs/inst/doc/ngenomeschips.Rnw
altcdfenvs/inst/doc/ngenomeschips.pdf
altcdfenvs/inst/exampleData
altcdfenvs/inst/exampleData/Plasmodium-Probeset-IDs.txt
altcdfenvs/inst/exampleData/sample.fasta
altcdfenvs/inst/exampleData/slamf_targets.RData
altcdfenvs/inst/internalData
altcdfenvs/inst/internalData/chipspecs.tab
altcdfenvs/man
altcdfenvs/man/AffyProbesMatch-class.Rd
altcdfenvs/man/CdfEnvAffy-class.Rd
altcdfenvs/man/appendCdfEnvAffy.Rd
altcdfenvs/man/buildCdfEnv.biostrings.Rd
altcdfenvs/man/cdfenv.Rd
altcdfenvs/man/cdfenvEx.Rd
altcdfenvs/man/copyCdfEnvAffy.Rd
altcdfenvs/man/countduplicated.Rd
altcdfenvs/man/geneNames.Rd
altcdfenvs/man/getxy.probeseq.Rd
altcdfenvs/man/index2xy.Rd
altcdfenvs/man/indexProbes.CdfEnvAffy.Rd
altcdfenvs/man/matchAffyProbes.Rd
altcdfenvs/man/plot.CdfEnvAffy.Rd
altcdfenvs/man/removeIndex.Rd
altcdfenvs/man/toHypergraph.Rd
altcdfenvs/man/unique.CdfEnvAffy.Rd
altcdfenvs/man/utils.FASTA.Rd
altcdfenvs/man/validAffyBatch.Rd
altcdfenvs/vignettes
altcdfenvs/vignettes/altcdfenvs.Rnw
altcdfenvs/vignettes/modify.Rnw
altcdfenvs/vignettes/ngenomeschips.Rnw