alternative CDF environments (aka mappings)


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Documentation for package ‘altcdfenvs’ version 2.2.0

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AffyProbesMatch-class Class "AffyProbesMatch"
appendCdfEnvAffy append probe sets to a CdfEnvAffy
buildCdfEnv.biostrings Build CDF environments
buildCdfEnv.matchprobes functions related to cdfenvs
CdfEnv functions related to cdfenvs
CdfEnvAffy-class Class "CdfEnvAffy"
cdfenvEx CdfEnvAffy
coerce,CdfEnvAffy,Cdf-method Class "CdfEnvAffy"
coerce,CdfEnvAffy,environment-method Class "CdfEnvAffy"
combine,AffyProbesMatch,AffyProbesMatch-method Class "AffyProbesMatch"
copyCdfEnvAffy make a copy of a CdfEnvAffy
countduplicated Count the number of times probes are used
countskip.FASTA.entries Functions to work with FASTA files / connections
geneNames,CdfEnvAffy-method Class "CdfEnvAffy"
geneNames.CdfEnvAffy get the names of the known probe sets
getCdfEnvAffy functions related to cdfenvs
getxy.probeseq A function to get the XY coordinates from a probes sequences data frame
grep.FASTA.entry Functions to work with FASTA files / connections
index2xy Functions to shuttle from indexes to XY coordinates
index2xy,CdfEnvAffy-method Class "CdfEnvAffy"
index2xy.CdfEnvAffy Functions to shuttle from indexes to XY coordinates
indexProbes,CdfEnvAffy,character-method Class "CdfEnvAffy"
indexProbes.CdfEnvAffy indexes for probes
matchAffyProbes Match the probes on an Affymetrix array
mmProbes Match the probes on an Affymetrix array
plot,CdfEnvAffy,missing-method Class "CdfEnvAffy"
plot.CdfEnvAffy A function to ‘plot’ a CdfEnvAffy
print.FASTA Functions to work with FASTA files / connections
printValidCdfEnvAffy Check validity of a CdfEnvAffy.
read.FASTA.entry Functions to work with FASTA files / connections
read.n.FASTA.entries Functions to work with FASTA files / connections
read.n.FASTA.headers Functions to work with FASTA files / connections
read.n.FASTA.sequences Functions to work with FASTA files / connections
removeIndex A function to remove probes in an environment
show,AffyProbesMatch-method Class "AffyProbesMatch"
show,CdfEnvAffy-method Class "CdfEnvAffy"
skip.FASTA.entry Functions to work with FASTA files / connections
toHypergraph Transform to an hypergraph
toHypergraph,AffyProbesMatch-method Class "AffyProbesMatch"
toHypergraph,CdfEnvAffy-method Class "CdfEnvAffy"
unique.CdfEnvAffy Remove duplicated elements from a CdfEnvAffy
validAffyBatch Check validity of a CdfEnvAffy.
validCdfEnvAffy Check validity of a CdfEnvAffy.
wrapCdfEnvAffy functions related to cdfenvs
write.FASTA Functions to work with FASTA files / connections
xy2index Functions to shuttle from indexes to XY coordinates
xy2index,CdfEnvAffy-method Class "CdfEnvAffy"
xy2index.CdfEnvAffy Functions to shuttle from indexes to XY coordinates
[,CdfEnvAffy-method Class "CdfEnvAffy"