# alternative CDF environments (aka probeset mappings)

## Documentation for package ‘altcdfenvs’ version 2.60.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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-method | Class "CdfEnvAffy"
combine-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-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-method | Class "CdfEnvAffy"
index2xy.CdfEnvAffy | Functions to shuttle from indexes to XY coordinates
indexProbes-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-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.entries.split | 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-method | Class "AffyProbesMatch"
show-method | Class "CdfEnvAffy"
skip.FASTA.entry | Functions to work with FASTA files / connections
toHypergraph | Transform to an hypergraph
toHypergraph-method | Class "AffyProbesMatch"
toHypergraph-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-method | Class "CdfEnvAffy"
xy2index.CdfEnvAffy | Functions to shuttle from indexes to XY coordinates
[-method | Class "CdfEnvAffy"