![[R logo]](../../../doc/html/logo.jpg)
| array.subset | Given an expression object get a particular subset of arrays defined by the phenoData |
| array.subset,AffyBatch-method | Given an expression object get a particular subset of arrays defined by the phenoData |
| array.subset,ExpressionSet-method | Given an expression object get a particular subset of arrays defined by the phenoData |
| clear.db.local | Display the contents/clear the contents of the local data directory |
| col.rd.bl | Use the X:MAP database to find annotated gene structure and generate a plot |
| db.local.info | Display the contents/clear the contents of the local data directory |
| details | Get detailed annotation for exons, transcripts and genes |
| exclude.probewise | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| exon.details | Get detailed annotation for exons, transcripts and genes |
| exon.to.gene | Map between probes, probesets, exons, transcripts and genes |
| exon.to.probeset | Map between probes, probesets, exons, transcripts and genes |
| exon.to.sequence | Map between probes, probesets, exons, transcripts and genes |
| exon.to.transcript | Map between probes, probesets, exons, transcripts and genes |
| exonic | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| exons.in.range | Given a set of chromosome coordinates, return the genomic features within |
| fc | Simple pariwise comparisons on exon expression data |
| fc,PC-method | Class "PC" represents the result of a simple pairwise comparison between two groups of arrays |
| filters | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| gene.details | Get detailed annotation for exons, transcripts and genes |
| gene.graph | Use the X:Map database to find annotated gene structure and generate a plot |
| gene.graph | Use the X:Map database to find annotated gene structure and generate a plot |
| gene.legend | Generate a colour bar to use as a legend |
| gene.strip | Use the X:MAP database to find annotated gene structure and generate a plot for multiple genes |
| gene.to.exon | Map between probes, probesets, exons, transcripts and genes |
| gene.to.exon.probeset | Map between probes, probesets, exons, transcripts and genes |
| gene.to.exon.probeset.expr | Map between probes, probesets, exons, transcripts and genes |
| gene.to.probeset | Map between probes, probesets, exons, transcripts and genes |
| gene.to.transcript | Map between probes, probesets, exons, transcripts and genes |
| genes.in.range | Given a set of chromosome coordinates, return the genomic features within |
| group.indices | Given an expression object get the array indices for a particular set of arrays |
| intergenic | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| intronic | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| is.exonic | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| is.intergenic | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| is.intronic | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| is.multitarget | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| mappings | Map between probes, probesets, exons, transcripts and genes |
| multitarget | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| pc | Simple pariwise comparisons on exon expression data |
| PC-class | Class "PC" represents the result of a simple pairwise comparison between two groups of arrays |
| plotGene | Use the X:MAP database to find annotated gene structure and generate a plot |
| probes.in.range | Given a set of chromosome coordinates, return the genomic features within |
| probeset.stats | Generates summary statistics showing intron, exon and gene hits for the spefied probeset list |
| probeset.to.exon | Map between probes, probesets, exons, transcripts and genes |
| probeset.to.gene | Map between probes, probesets, exons, transcripts and genes |
| probeset.to.probe | Map between probes, probesets, exons, transcripts and genes |
| probeset.to.transcript | Map between probes, probesets, exons, transcripts and genes |
| probesets.in.range | Given a set of chromosome coordinates, return the genomic features within |
| ps.value | Use the X:MAP database to find annotated gene structure and generate a plot for multiple genes |
| read.exon | Read a Set of .CEL Files and Phenotypic Data representing exon arrays |
| select.probewise | Filter vectors of Affymetrix Exon array probeset names according to where they target |
| si | Calculate the splicing index |
| splicing.index | Calculate the splicing index |
| symbol.to.gene | Map between probes, probesets, exons, transcripts and genes |
| symbol.to.probeset | Map between probes, probesets, exons, transcripts and genes |
| transcript.details | Get detailed annotation for exons, transcripts and genes |
| transcript.to.exon | Map between probes, probesets, exons, transcripts and genes |
| transcript.to.gene | Map between probes, probesets, exons, transcripts and genes |
| transcript.to.probeset | Map between probes, probesets, exons, transcripts and genes |
| transcripts.in.range | Given a set of chromosome coordinates, return the genomic features within |
| tt | Simple pariwise comparisons on exon expression data |
| tt,PC-method | Class "PC" represents the result of a simple pairwise comparison between two groups of arrays |
| value.to.colour | Use the X:MAP database to find annotated gene structure and generate a plot for multiple genes |
| x.rma | Sample exonmap dataset |
| xmapConnect | Connect/disconnect to an xmap database |
| xmapDatabase | Connect/disconnect to an xmap database |
| xmapDisconnect | Connect/disconnect to an xmap database |
| xmapExon | Open a browser window at the X:Map database, centered on the specified feature |
| xmapGene | Open a browser window at the X:Map database, centered on the specified feature |
| xmapProbeset | Open a browser window at the X:Map database, centered on the specified feature |
| xmapTranscript | Open a browser window at the X:Map database, centered on the specified feature |
| [,PC-method | Class "PC" represents the result of a simple pairwise comparison between two groups of arrays |
| [<-,PC-method | Class "PC" represents the result of a simple pairwise comparison between two groups of arrays |