Entry: CdfEnvAffy-class
Aliases: CdfEnvAffy-class geneNames,CdfEnvAffy-method index2xy,CdfEnvAffy-method indexProbes,CdfEnvAffy,character-method plot,CdfEnvAffy,missing-method show,CdfEnvAffy-method xy2index,CdfEnvAffy-method coerce,CdfEnvAffy,environment-method coerce,CdfEnvAffy,Cdf-method [,CdfEnvAffy-method
Keywords: classes
Description: Class "CdfEnvAffy"
URL: ../../../library/altcdfenvs/html/CdfEnvAffy-class.html

Entry: appendCdfEnvAffy
Aliases: appendCdfEnvAffy
Keywords: manip
Description: append probe sets to a CdfEnvAffy
URL: ../../../library/altcdfenvs/html/appendCdfEnvAffy.html

Entry: cdfenvs
Aliases: wrapCdfEnvAffy getCdfEnvAffy buildCdfEnv.matchprobes CdfEnv
Keywords: manip
Description: functions related to cdfenvs
URL: ../../../library/altcdfenvs/html/cdfenv.html

Entry: cdfenvEx
Aliases: cdfenvEx
Keywords: datasets
Description: CdfEnvAffy
URL: ../../../library/altcdfenvs/html/cdfenvEx.html

Entry: copyCdfEnvAffy
Aliases: copyCdfEnvAffy
Keywords: manip
Description: make a copy of a CdfEnvAffy
URL: ../../../library/altcdfenvs/html/copyCdfEnvAffy.html

Entry: countduplicated
Aliases: countduplicated
Keywords: manip
Description: Count the number of times probes are used
URL: ../../../library/altcdfenvs/html/countduplicated.html

Entry: geneNames.CdfEnvAffy
Aliases: geneNames.CdfEnvAffy
Keywords: manip
Description: get the names of the known probe sets
URL: ../../../library/altcdfenvs/html/geneNames.html

Entry: getxy.probeseq
Aliases: getxy.probeseq
Keywords: manip
Description: A function to get the XY coordinates from a probes sequences data frame
URL: ../../../library/altcdfenvs/html/getxy.probeseq.html

Entry: index2xy
Aliases: index2xy index2xy.CdfEnvAffy xy2index xy2index.CdfEnvAffy
Keywords: manip
Description: Functions to shuttle from indexes to XY coordinates
URL: ../../../library/altcdfenvs/html/index2xy.html

Entry: indexProbes.CdfEnvAffy
Aliases: indexProbes.CdfEnvAffy
Keywords: manip
Description: indexes for probes
URL: ../../../library/altcdfenvs/html/indexProbes.CdfEnvAffy.html

Entry: plot.CdfEnvAffy
Aliases: plot.CdfEnvAffy
Keywords: hplot
Description: A function to 'plot' a CdfEnvAffy
URL: ../../../library/altcdfenvs/html/plot.CdfEnvAffy.html

Entry: removeIndex
Aliases: removeIndex
Keywords: manip
Description: A function to remove probes in an environment
URL: ../../../library/altcdfenvs/html/removeIndex.html

Entry: unique.CdfEnvAffy
Aliases: unique.CdfEnvAffy
Keywords: manip
Description: Remove duplicated elements from a CdfEnvAffy
URL: ../../../library/altcdfenvs/html/unique.CdfEnvAffy.html

Entry: read.FASTA.entry
Aliases: read.FASTA.entry print.FASTA write.FASTA skip.FASTA.entry read.n.FASTA.entries read.n.FASTA.headers read.n.FASTA.sequences read.n.FASTA.entries.split countskip.FASTA.entries read.FASTA.entry grep.FASTA.entry
Keywords: manip IO connection
Description: Functions to work with FASTA files / connections
URL: ../../../library/altcdfenvs/html/utils.FASTA.html

Entry: validAffyBatch
Aliases: validAffyBatch validCdfEnvAffy printValidCdfEnvAffy
Keywords: manip
Description: Check validity of a CdfEnvAffy.
URL: ../../../library/altcdfenvs/html/validAffyBatch.html
