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


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Documentation for package ‘annmap’ version 1.22.0

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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