altcdfenvs: alternative CDF environments (aka probeset mappings)
Version 2.38.0

Convenience data structures and functions to handle cdfenvs

Browse man pages Browse package API and functions Browse package files

AuthorLaurent Gautier <lgautier@gmail.com>
Bioconductor views Annotation Microarray OneChannel Preprocessing ProprietaryPlatforms QualityControl Transcription
Date of publicationNone
MaintainerLaurent Gautier <lgautier@gmail.com>
LicenseGPL (>= 2)
Version2.38.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("altcdfenvs")

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.

Functions

AffyProbesMatch-class Man page
CdfEnv Man page
CdfEnvAffy-class Man page
[,CdfEnvAffy,character,missing,missing-method Man page
appendCdfEnvAffy Man page Source code
buildCdfEnv.biostrings Man page Source code
buildCdfEnv.matchprobes Man page Source code
cdfenvEx Man page
coerce,CdfEnvAffy,Cdf-method Man page
coerce,CdfEnvAffy,environment-method Man page
combine,AffyProbesMatch,AffyProbesMatch-method Man page
copyCdfEnvAffy Man page Source code
countduplicated Man page Source code
countskip.FASTA.entries Man page Source code
geneNames,CdfEnvAffy-method Man page
geneNames.AltAffyBatch Man page
geneNames.CdfEnvAffy Man page Source code
getCdfEnvAffy Man page Source code
getxy.probeseq Man page Source code
grep.FASTA.entry Man page Source code
index2xy Man page
index2xy,CdfEnvAffy-method Man page
index2xy.AltAffyBatch Man page
index2xy.CdfEnvAffy Man page Source code
indexProbes,CdfEnvAffy,character-method Man page
indexProbes.AltAffyBatch Man page
indexProbes.CdfEnvAffy Man page Source code
matchAffyProbes Man page Source code
mmProbes Man page Source code
plot,CdfEnvAffy,missing-method Man page
plot.CdfEnvAffy Man page Source code
print.FASTA Man page Source code
printValidCdfEnvAffy Man page Source code
read.FASTA.entry Man page Man page Source code
read.n.FASTA.entries Man page Source code
read.n.FASTA.entries.split Man page Source code
read.n.FASTA.headers Man page Source code
read.n.FASTA.sequences Man page Source code
removeIndex Man page Source code
show,AffyProbesMatch-method Man page
show,CdfEnvAffy-method Man page
skip.FASTA.entry Man page Source code
toHypergraph Man page Source code
toHypergraph,AffyProbesMatch-method Man page
toHypergraph,CdfEnvAffy-method Man page
unique.CdfEnvAffy Man page Source code
validAffyBatch Man page Source code
validCdfEnvAffy Man page Source code
wrapCdfEnvAffy Man page Source code
write.FASTA Man page Source code
xy2index Man page
xy2index,CdfEnvAffy-method Man page
xy2index.AltAffyBatch Man page
xy2index.CdfEnvAffy Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/CdfEnv.R
R/appendCdfEnvAffy.R
R/buildCdfEnv.biostrings.R
R/buildCdfEnv.matchprobes.R
R/cdfenvs.R
R/copyCdfEnvAffy.R
R/readFASTA.R
R/removeIndex.R
R/unique.CdfEnvAffy.R
build
build/vignette.rds
data
data/cdfenvEx.rda
inst
inst/CITATION
inst/UnitTests
inst/UnitTests/AffyProbesMatch_test.R
inst/doc
inst/doc/altcdfenvs.R
inst/doc/altcdfenvs.Rnw
inst/doc/altcdfenvs.pdf
inst/doc/modify.R
inst/doc/modify.Rnw
inst/doc/modify.pdf
inst/doc/ngenomeschips.R
inst/doc/ngenomeschips.Rnw
inst/doc/ngenomeschips.pdf
inst/exampleData
inst/exampleData/Plasmodium-Probeset-IDs.txt
inst/exampleData/sample.fasta
inst/exampleData/slamf_targets.RData
inst/internalData
inst/internalData/chipspecs.tab
man
man/AffyProbesMatch-class.Rd
man/CdfEnvAffy-class.Rd
man/appendCdfEnvAffy.Rd
man/buildCdfEnv.biostrings.Rd
man/cdfenv.Rd
man/cdfenvEx.Rd
man/copyCdfEnvAffy.Rd
man/countduplicated.Rd
man/geneNames.Rd
man/getxy.probeseq.Rd
man/index2xy.Rd
man/indexProbes.CdfEnvAffy.Rd
man/matchAffyProbes.Rd
man/plot.CdfEnvAffy.Rd
man/removeIndex.Rd
man/toHypergraph.Rd
man/unique.CdfEnvAffy.Rd
man/utils.FASTA.Rd
man/validAffyBatch.Rd
vignettes
vignettes/altcdfenvs.Rnw
vignettes/modify.Rnw
vignettes/ngenomeschips.Rnw
altcdfenvs documentation built on May 20, 2017, 9:15 p.m.