alternative CDF environments (aka probeset mappings)
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Documentation for package ‘altcdfenvs’ version 2.69.0
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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-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" |