annotateRanges {FRASER}R Documentation

Annotates the given FraserDataSet with the HGNC symbol with biomaRt

Description

Annotates the given FraserDataSet with the HGNC symbol with biomaRt

Usage

annotateRanges(
  fds,
  feature = "hgnc_symbol",
  featureName = feature,
  biotype = list("protein_coding"),
  ensembl = NULL,
  GRCh = 37
)

annotateRangesWithTxDb(
  fds,
  feature = "SYMBOL",
  featureName = "hgnc_symbol",
  keytype = "ENTREZID",
  txdb = NULL,
  orgDb = NULL
)

Arguments

fds

FraserDataSet

feature

Defines which feature (default is HGNC symbol) should be annotated.

featureName

Name of the feature in the FraserDataSet mcols.

biotype

The biotype.

ensembl

The ensembl that should be used. If NULL, the default one is used (hsapiens_gene_ensembl, GRCh37).

GRCh

GRCh version to connect to. If this is NULL, then the current GRCh38 is used. Otherwise, this can only be 37 (default) at the moment (see useEnsembl).

keytype

The type of gene IDs in the TxDb object (see AnnotationDbi::keytypes(orgDb) for a list of available ID types).

txdb

A TxDb object. If this is NULL, then the default one is used, currently this is TxDb.Hsapiens.UCSC.hg19.knownGene.

orgDb

An orgDb object If this is NULL, then the default one is used, currently this is org.Hs.eg.db.

Value

FraserDataSet

Examples


fds <- createTestFraserDataSet()

## Not run: 
### Two ways to annotage ranges with gene names: 
# either using biomart:
fds <- annotateRanges(fds, GRCh=NULL)
rowRanges(fds, type="psi5")[,"hgnc_symbol"]
 
# or with a TxDb object
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
require(org.Hs.eg.db)
orgDb <- org.Hs.eg.db
fds <- annotateRangesWithTxDb(fds, txdb=txdb, orgDb=orgDb)

rowRanges(fds, type="psi5")[,"hgnc_symbol"]

## End(Not run)


[Package FRASER version 1.0.2 Index]