annmap.to: annmap 'to' functions

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

Description

Map between the different levels of annotation in Annmap. For example, given a vector of gene identifiers, geneToExon will return the exons in those genes.

Usage

  arrayToProbeset( ids, as.vector=FALSE )
  domainToGene( ids, as.vector=FALSE )
  domainToProbeset( ids, as.vector=FALSE )
  domainToProtein( ids, as.vector=FALSE )
  domainToTranscript( ids, as.vector=FALSE )
  estExonToEstGene( ids, as.vector=FALSE )
  estExonToEstTranscript( ids, as.vector=FALSE )
  estExonToProbeset( ids, as.vector=FALSE )
  estGeneToEstExon( ids, as.vector=FALSE )
  estGeneToEstTranscript( ids, as.vector=FALSE )
  estGeneToProbeset( ids, as.vector=FALSE )
  estTranscriptToEstExon( ids, as.vector=FALSE )
  estTranscriptToEstGene( ids, as.vector=FALSE )
  estTranscriptToProbeset( ids, as.vector=FALSE )
  exonToGene( ids, as.vector=FALSE )
  exonToProbeset( ids, as.vector=FALSE )
  exonToTranscript( ids, as.vector=FALSE )
  geneToDomain( ids, as.vector=FALSE )
  geneToExon( ids, as.vector=FALSE )
  geneToExonProbeset( ids, as.vector=FALSE, probes.min=4 )
  geneToExonProbesetExpr( x, ids, probes.min=4 )
  geneToProbeset( ids, as.vector=FALSE )
  geneToProtein( ids, as.vector=FALSE )
  geneToSymbol( ids )
  geneToSynonym( ids, as.vector=FALSE )
  geneToTranscript( ids, as.vector=FALSE )
  predictionTranscriptToPredictionExon( ids )
  predictionTranscriptToProbeset( ids, as.vector=FALSE )
  probeToHit( ids, as.data.frame=FALSE )
  probeToProbeset( ids, as.vector=FALSE )
  probesetToCdnatranscript( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToDomain( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToEstExon( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToEstGene( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToEstTranscript( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToExon( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToGene( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToHit( ids, as.data.frame=FALSE, rm.unreliable=TRUE )
  probesetToPredictionTranscript( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToProbe( ids, as.vector=FALSE )
  probesetToProtein( ids, as.vector=FALSE, rm.unreliable=TRUE )
  probesetToTranscript( ids, as.vector=FALSE, rm.unreliable=TRUE )
  proteinToDomain( ids, as.vector=FALSE )
  proteinToGene( ids, as.vector=FALSE )
  proteinToProbeset( ids, as.vector=FALSE )
  proteinToTranscript( ids, as.vector=FALSE )
  symbolToEstGene( ids, as.vector=FALSE )
  symbolToEstTranscript( ids, as.vector=FALSE )
  symbolToGene( ids, as.vector=FALSE )
  symbolToTranscript( ids, as.vector=FALSE )
  synonymToEstGene( ids, as.vector=FALSE )
  synonymToEstTranscript( ids, as.vector=FALSE )
  synonymToGene( ids, as.vector=FALSE )
  synonymToTranscript( ids, as.vector=FALSE )
  transcriptToCdnaprobeset( ids, as.vector=FALSE )
  transcriptToDomain( ids, as.vector=FALSE )
  transcriptToExon( ids, as.vector=FALSE )
  transcriptToExonProbeset( ids, as.vector=FALSE, probes.min=4 )
  transcriptToGene( ids, as.vector=FALSE )
  transcriptToProbeset( ids, as.vector=FALSE )
  transcriptToProtein( ids, as.vector=FALSE )
  transcriptToSynonym( ids, as.vector=FALSE )
  transcriptToTranslatedprobes( ids )

Arguments

as.vector	If TRUE returns a vector of database identifiers. If FALSE returns a link{RangedData} object containing detailed annotation.
as.data.frame	Where a vector is inappropriate for the data type, the option to return the data as a plain data.frame in place of a GRanges object is given.
ids	Database identifiers to map from. Can be either a vector of database identifiers, or a GRanges object.
probes.min	How many probes need to match before the probeset is returned.
rm.unreliable	If TRUE, the input probeset list is filtered, and all unreliable probesets are removed.
x	An ExpressionSet object or a matrix containing expression data. If the latter, then the rownames must specify the exon array probeset names.

Details

In most cases, these functions should be self-explantory. However, by default, the mappings involving probes and probesets do some filtering of the data. This means that probesets which have one or more probes that don't match to the genome, or which match to multiple loci, are removed (see unreliable for more details).

The function transcriptToTranslatedprobes returns a list of GRanges objects (one for each transcript) containing each probe that hits that translated transcripts and the relative start and end locations.

Value

Results in an GRanges object, one row per feature, containing detailed annotations, or a vector, as defined by as.vector.

Author(s)

Tim Yates

See Also

annmapDetails
annmapAll
annmapRange
annmapUtils
annmapFilters
link{GRanges}

Examples

  if(interactive()) {
    annmapConnect()
    geneToExon(symbolToGene("TP53"))
  } 

annmap documentation built on Nov. 8, 2020, 7:43 p.m.