R: Annotates the given FraserDataSet with the HGNC symbol with...

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]