annotateTranscripts | R Documentation |
Annotate transcripts
annotateTranscripts(txdb, annotationPackage = NULL, by = c("tx","gene"), codingOnly=FALSE, verbose = TRUE, requireAnnotation = FALSE, mappingInfo = NULL, simplifyGeneID = FALSE)
txdb |
A |
annotationPackage |
An annotation data package from which to obtain gene/transcript
annotation. For example |
by |
Should we create a |
codingOnly |
Should we exclude all the non-coding transcripts. |
verbose |
logical value. If 'TRUE', it writes out some messages indicating progress. If 'FALSE' nothing should be printed. |
requireAnnotation |
logical value. If 'TRUE' function will stop if no annotation package is successfully loaded. |
mappingInfo |
a named list with elements 'column', 'keytype' and 'multiVals'. If specified
this information will be used with mapIds when mapping
the gene ids using |
simplifyGeneID |
logical value. If 'TRUE', gene ids will be shortened to before a dot is present in the id. This is useful for changing GENCODE gene ids to ENSEMBL ids. |
This function prepares a GRanges
for the matchGenes
function. It adds information and in particular adds exons information
to each gene/transcript.
A 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.
Harris Jaffee and Rafael A. Irizarry. 'mappingInfo' and 'simplifyGeneID' contributed by Leonardo Collado-Torres.
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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