AllelicImbalance (version 1.10.2)

annotation-wrappers: AnnotationDb wrappers

Description

These functions acts as wrappers to retrieve information from annotation database objects (annotationDb objects) or (transcriptDb objects)

Usage

getGenesFromAnnotation(OrgDb, GR, leftFlank = 0, rightFlank = 0,
  getUCSC = FALSE, verbose = FALSE)
getGenesVector(OrgDb, GR, leftFlank = 0, rightFlank = 0, verbose = FALSE)
getExonsFromAnnotation(TxDb, GR, leftFlank = 0, rightFlank = 0,
  verbose = FALSE)
getExonsVector(TxDb, GR, leftFlank = 0, rightFlank = 0, verbose = FALSE)
getTranscriptsFromAnnotation(TxDb, GR, leftFlank = 0, rightFlank = 0,
  verbose = FALSE)
getTranscriptsVector(TxDb, GR, leftFlank = 0, rightFlank = 0,
  verbose = FALSE)
getCDSFromAnnotation(TxDb, GR, leftFlank = 0, rightFlank = 0,
  verbose = FALSE)
getCDSVector(TxDb, GR, leftFlank = 0, rightFlank = 0, verbose = FALSE)
getAnnotationDataFrame(GR, strand = "+", annotationType = NULL,
  OrgDb = NULL, TxDb = NULL, verbose = FALSE)

Arguments

OrgDb

An OrgDb object

GR

A GenomicRanges object with sample area

leftFlank

An integer specifying number of additional nucleotides around the SNPs for the leftFlank

rightFlank

An integer specifying number of additional nucleotides around the SNPs for the rightFlank

getUCSC

A logical indicating if UCSC transcript IDs should also be retrieved

verbose

A logical making the functions more talkative

TxDb

A transcriptDb object

strand

Two options,'+' or '-'

annotationType

select one or more from 'gene', 'exon', 'transcript', 'cds'.

Value

• GRanges object with ranges over the genes in the region.

  The getGenesVector function will return a character vector where each element are gene symbols separated by commaGRanges object with ranges over the exons in the region.

  The getTranscriptsFromAnnotation function will return a GRanges object with ranges over the transcripts in the region.

  The getCDSFromAnnotation function will return a GRanges object with ranges over the CDSFs in the region.

  The getExonsVector function will return a character vector where each element are exons separated by comma

  The getTranscriptsVector function will return a character vector where each element are transcripts separated by comma

  The getCDSVector function will return a character vector where each element are CDSs separated by comma

  The getAnnotationDataFrame function will return a data.frame with annotations. This function is used internally by i.e. the barplot-function

Details

These functions retrieve regional annotation from OrgDb or TxDb objects, when given GRanges objects.

Examples

data(ASEset)
  require(org.Hs.eg.db)
  require(TxDb.Hsapiens.UCSC.hg19.knownGene)
  OrgDb <- org.Hs.eg.db
  TxDb <- TxDb.Hsapiens.UCSC.hg19.knownGene

  #use for example BcfFiles as the source for SNPs of interest
  GR <- rowRanges(ASEset)
  #get annotation
  g <- getGenesFromAnnotation(OrgDb,GR)
  e <- getExonsFromAnnotation(TxDb,GR)
  t <- getTranscriptsFromAnnotation(TxDb,GR)
  c <- getCDSFromAnnotation(TxDb,GR)