annotation-wrappers: AnnotationDb wrappers

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

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'.

Details

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

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 comma

GRanges 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

Author(s)

Jesper R. Gadin, Lasse Folkersen

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)
  

pappewaio/AllelicImbalance documentation built on April 11, 2020, 2:58 a.m.