High level analysis of Affymetrix exon array data


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Documentation for package ‘exonmap’ version 2.0.03

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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.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.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