annotation-wrappers {AllelicImbalance} | R Documentation |
These functions acts as wrappers to retrieve information from annotation
database objects (annotationDb objects
) or (transcriptDb
objects
)
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)
OrgDb |
An |
GR |
A |
leftFlank |
An |
rightFlank |
An |
getUCSC |
A |
verbose |
A |
TxDb |
A |
strand |
Two options,'+' or '-' |
annotationType |
select one or more from 'gene', 'exon', 'transcript', 'cds'. |
These functions retrieve regional annotation from OrgDb or TxDb objects, when given GRanges objects.
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
Jesper R. Gadin, Lasse Folkersen
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)