# Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

## Documentation for package ‘annmap’ version 1.40.0

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

## Help Pages

A C D E G H I N P S T U

annmap-package | Provide access to the Annmap annotation database

## -- A --

allArrays | annmap 'all' functions
allChromosomes | annmap 'all' functions
allDomains | annmap 'all' functions
allEstExons | annmap 'all' functions
allEstGenes | annmap 'all' functions
allEstTranscripts | annmap 'all' functions
allExons | annmap 'all' functions
allGenes | annmap 'all' functions
allPredictionTranscripts | annmap 'all' functions
allProbes | annmap 'all' functions
allProbesets | annmap 'all' functions
allProteins | annmap 'all' functions
allSymbols | annmap 'all' functions
allSynonyms | annmap 'all' functions
allTranscripts | annmap 'all' functions
annmap | Provide access to the Annmap annotation database
annmapAddConnection | annmap 'utils' functions
annmapAll | annmap 'all' functions
annmapClearCache | annmap 'utils' functions
annmapConnect | annmap 'utils' functions
annmapDetails | annmap 'details' functions
annmapDisconnect | annmap 'utils' functions
annmapEnv | annmap 'env' functions
annmapFilters | annmap 'filter' functions
annmapGenePlot | annmap 'utils' functions
annmapGetParam | annmap 'env' functions
annmapRange | annmap 'range' functions
annmapRangeApply | annmap 'utils' functions
annmapSeqname | Seqnames manipulation functions
annmapSetParam | annmap 'env' functions
annmapTo | annmap 'to' functions
annmapToggleCaching | annmap 'utils' functions
annmapUtils | annmap 'utils' functions
arrayDetails | annmap 'details' functions
arrayToProbeset | annmap 'to' functions
arrayType | annmap 'utils' functions

## -- C --

chromosomeDetails | annmap 'details' functions
codingProbesets | annmap coding functions
convertBamToRle | Plotting BAM file data alongside the features of a chromosome

## -- D --

domainDetails | annmap 'details' functions
domainInRange | annmap 'range' functions
domainInRange-method | annmap 'range' functions
domainToGene | annmap 'to' functions
domainToProbeset | annmap 'to' functions
domainToProtein | annmap 'to' functions
domainToTranscript | annmap 'to' functions

## -- E --

estExonDetails | annmap 'details' functions
estExonInRange | annmap 'range' functions
estExonInRange-method | annmap 'range' functions
estExonToEstGene | annmap 'to' functions
estExonToEstTranscript | annmap 'to' functions
estExonToProbeset | annmap 'to' functions
estGeneDetails | annmap 'details' functions
estGeneInRange | annmap 'range' functions
estGeneInRange-method | annmap 'range' functions
estGeneToEstExon | annmap 'to' functions
estGeneToEstTranscript | annmap 'to' functions
estGeneToProbeset | annmap 'to' functions
estTranscriptDetails | annmap 'details' functions
estTranscriptInRange | annmap 'range' functions
estTranscriptInRange-method | annmap 'range' functions
estTranscriptToEstExon | annmap 'to' functions
estTranscriptToEstGene | annmap 'to' functions
estTranscriptToProbeset | annmap 'to' functions
exonDetails | annmap 'details' functions
exonic | annmap 'filter' functions
exonInRange | annmap 'range' functions
exonInRange-method | annmap 'range' functions
exonToGene | annmap 'to' functions
exonToProbeset | annmap 'to' functions
exonToTranscript | annmap 'to' functions

## -- G --

geneDetails | annmap 'details' functions
geneInRange | annmap 'range' functions
geneInRange-method | annmap 'range' functions
generalisedNameToEnsembl | Seqnames manipulation functions
generalisedNameToNCBI | Seqnames manipulation functions
generateBridgeData | Plotting BAM file data alongside the features of a chromosome
geneToDomain | annmap 'to' functions
geneToExon | annmap 'to' functions
geneToExonProbeset | annmap 'to' functions
geneToExonProbesetExpr | annmap 'to' functions
geneToGeneRegionTrack | annmap 'utils' functions
geneToProbeset | annmap 'to' functions
geneToProtein | annmap 'to' functions
geneToSymbol | annmap 'to' functions
geneToSynonym | annmap 'to' functions
geneToTranscript | annmap 'to' functions
genomeToProteinCoords | annmap co-ordinate mapping functions
genomeToTranscriptCoords | annmap co-ordinate mapping functions
genomicExonDepthPlot | Plotting a section of a chromosome.
genomicPlot | Plotting a section of a chromosome.
genomicProbePlot | Plotting a section of a chromosome.

## -- H --

hasProbes | annmap 'filter' functions
hasProbesAtleast | annmap 'filter' functions
hasProbesBetween | annmap 'filter' functions
hasProbesIn | annmap 'filter' functions

## -- I --

intergenic | annmap 'filter' functions
intronic | annmap 'filter' functions
isExonic | annmap 'filter' functions
isIntergenic | annmap 'filter' functions
isIntronic | annmap 'filter' functions
isUnreliable | annmap 'filter' functions

## -- N --

ngsBridgePlot | Plotting BAM file data alongside the features of a chromosome
ngsTraceLabel | Plotting BAM file data alongside the features of a chromosome
ngsTracePlotter | Plotting BAM file data alongside the features of a chromosome
ngsTraceScale | Plotting BAM file data alongside the features of a chromosome
nonIntronicGeneLength | annmap coding functions
nonIntronicTranscriptLength | annmap coding functions

## -- P --

predictionTranscriptDetails | annmap 'details' functions
predictionTranscriptInRange | annmap 'range' functions
predictionTranscriptInRange-method | annmap 'range' functions
predictionTranscriptToPredictionExon | annmap 'to' functions
predictionTranscriptToProbeset | annmap 'to' functions
probeDetails | annmap 'details' functions
probeInRange | annmap 'range' functions
probeInRange-method | annmap 'range' functions
probesetDetails | annmap 'details' functions
probesetInRange | annmap 'range' functions
probesetInRange-method | annmap 'range' functions
probesetToCdnatranscript | annmap 'to' functions
probesetToDomain | annmap 'to' functions
probesetToEstExon | annmap 'to' functions
probesetToEstGene | annmap 'to' functions
probesetToEstTranscript | annmap 'to' functions
probesetToExon | annmap 'to' functions
probesetToGene | annmap 'to' functions
probesetToHit | annmap 'to' functions
probesetToPredictionTranscript | annmap 'to' functions
probesetToProbe | annmap 'to' functions
probesetToProtein | annmap 'to' functions
probesetToTranscript | annmap 'to' functions
probeToHit | annmap 'to' functions
probeToProbeset | annmap 'to' functions
proteinCoordsToGenome | annmap co-ordinate mapping functions
proteinDetails | annmap 'details' functions
proteinInRange | annmap 'range' functions
proteinInRange-method | annmap 'range' functions
proteinToDomain | annmap 'to' functions
proteinToGene | annmap 'to' functions
proteinToProbeset | annmap 'to' functions
proteinToTranscript | annmap 'to' functions

## -- S --

seqnameMapping | Seqnames manipulation functions
seqnamesToEnsembl | Seqnames manipulation functions
seqnamesToNCBI | Seqnames manipulation functions
spliceGroupIndex | Splice indexing
spliceIndex | Splice indexing
strandAsInteger | annmap 'utils' functions
symbolToEstGene | annmap 'to' functions
symbolToEstTranscript | annmap 'to' functions
symbolToGene | annmap 'to' functions
symbolToTranscript | annmap 'to' functions
synonymDetails | annmap 'details' functions
synonymToEstGene | annmap 'to' functions
synonymToEstTranscript | annmap 'to' functions
synonymToGene | annmap 'to' functions
synonymToTranscript | annmap 'to' functions

## -- T --

transcriptCoordsToGenome | annmap co-ordinate mapping functions
transcriptDetails | annmap 'details' functions
transcriptInRange | annmap 'range' functions
transcriptInRange-method | annmap 'range' functions
transcriptToCdnaprobeset | annmap 'to' functions
transcriptToCodingExon | annmap coding functions
transcriptToCodingRange | annmap coding functions
transcriptToDomain | annmap 'to' functions
transcriptToExon | annmap 'to' functions
transcriptToExonProbeset | annmap 'to' functions
transcriptToGene | annmap 'to' functions
transcriptToProbeset | annmap 'to' functions
transcriptToProtein | annmap 'to' functions
transcriptToSynonym | annmap 'to' functions
transcriptToTranslatedprobes | annmap 'to' functions
transcriptToUtrExon | annmap coding functions
transcriptToUtrRange | annmap coding functions

## -- U --

unreliable | annmap 'filter' functions
utrProbesets | annmap coding functions