annotateRanges {FRASER} | R Documentation |
Annotates the given FraserDataSet with the HGNC symbol with biomaRt
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 )
fds |
FraserDataSet |
feature |
Defines which feature (default is HGNC symbol) should be
annotated. Has to be the |
featureName |
The column name of the feature in the FraserDataSet mcols. |
biotype |
The biotype for |
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 |
keytype |
The keytype or column name of gene IDs in the |
txdb |
A |
orgDb |
An |
FraserDataSet
fds <- createTestFraserDataSet() ### Two ways to annotage ranges with gene names: # either using biomart with GRCh38 try({ fds <- annotateRanges(fds, GRCh=38) rowRanges(fds, type="psi5")[,c("hgnc_symbol")] }) # either using biomart with GRCh37 try({ fds <- annotateRanges(fds, featureName="hgnc_symbol_37", GRCh=37) rowRanges(fds, type="psi5")[,c("hgnc_symbol_37")] }) # or with a provided 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"]