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annotateTranscripts(txdb, annotationPackage = NULL, by = c("tx","gene"), codingOnly=FALSE, verbose = TRUE, requireAnnotation = FALSE)
TxDb
database object such as TxDb.Hsapiens.UCSC.hg19.knownGene
org.Hs.eg.db
. If none is provided the
function tries to infer it from species(txdb)
and if it can't it
proceeds without annotation unless requireAnnotation = TRUE
.
GRanges
of transcripts (tx
) or genes (gene
).
GRanges
object with an attribute description
set to
annotatedTranscripts
. The following columns are added.
seqinfo
is the information returned by
seqinfo
, CSS
is the coding region
start, CSE
is the coding region end, Tx
is the transcript
ID used in TxDb, Entrez
is the Entrez ID, Gene
is the gene
symbol, Refseq
is the RefSeq annotation, Nexons
is the
number of exons, Exons
is an IRanges
with the exon information.
GRanges
for the matchGenes
function. It adds information and in particular adds exons information
to each gene/transcript.
matchGenes
## Not run:
# library("TxDb.Hsapiens.UCSC.hg19.knownGene")
# genes <- annotateTranscripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
#
# ##and to avoid guessing the annotation package:
# genes <- annotateTranscripts(TxDb.Hsapiens.UCSC.hg19.knownGene,annotation="org.Hs.eg.db")
#
# ## End(Not run)
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