High level analysis of Affymetrix exon array data


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Documentation for package `exonmap' version 1.0.07

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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,exprSet-method Given an expression object get a particular subset of arrays defined by the phenoData
col.rd.bl Use the X:MAP database to find annotated gene structure and generate a plot
dbHuman Switching between databases
dbMouse Switching between databases
exclude.probewise Filtering of lists of probesets
exon.details Use the X:MAP database to get detailed annotation for genes, transcripts and exons
exon.to.gene Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
exon.to.probeset Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
exon.to.transcript Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
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
fval Find probesets involved in differential splicing for multiple treatments
fval,Splanova-method Class "Splanova" represents the result of a splicing anova calculations
gene.details Use the X:MAP database to get detailed annotation for genes, transcripts and exons
gene.legend Add a colour bar to an X:MAP gene plot
gene.strip Use the X:MAP database to find annotated gene structure and generate a plot for multiple genes
gene.to.exon Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
gene.to.exon.probeset Using X:MAP database to translate genes into exons and probesets
gene.to.probeset Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
gene.to.transcript Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
genes.in.range Find probesets and genes by location
group.indices Given an expression object get the array indices for a particular set of arrays
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
plot.gene Use the X:MAP database to find annotated gene structure and generate a plot
plot.gene.graph Use the X:MAP database to find annotated gene structure and generate a plot
probes.only.in.range Find probesets and genes by location
probeset.stats Generates summary statistics showing intron, exon and gene hits for the spefied probeset list
probeset.to.exon Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
probeset.to.gene Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
probeset.to.probe Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
probeset.to.transcript Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
probesets.in.eset Filtering of lists of probesets
probesets.in.range Find probesets and genes by location
read.exon Read a Set of .CEL Files and Phenotypic Data representing exon arrays
select.probewise Filtering of lists of probesets
showXmapDatabase Switching between databases
sig Find probesets involved in differential splicing for multiple treatments
sig,Splanova-method Class "Splanova" represents the result of a splicing anova calculations
splanova Find probesets involved in differential splicing for multiple treatments
Splanova-class Class "Splanova" represents the result of a splicing anova calculations
splicing.index Find probesets involved in differential splicing for two treatments
symbol.to.gene Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
symbol.to.probeset Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
transcript.details Use the X:MAP database to get detailed annotation for genes, transcripts and exons
transcript.to.exon Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
transcript.to.gene Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
transcript.to.probeset Use the X:MAP database to translate between genes, transcripts, exons, probesets and probes
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
x.rma Sample exonmap dataset
xmapDatabase Switching between databases
xmapExon Linking to X:MAP browser
xmapGene Linking to X:MAP browser
xmapProbeset Linking to X:MAP browser
xmapTranscript Linking to X:MAP browser
[,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