Dear Bioc annotation team,
Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g. for
BRCA1; ENSG00000012048; entrez:672
via
> genes(TxDb.Hsapiens.UCSC.hg38.knownGene, vals=list(gene_id="672"))
gives me:
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | gene_id
<Rle> <IRanges> <Rle> | <character>
672 chr17 [43044295, 43170403] - | 672
-------
seqinfo: 455 sequences (1 circular) from hg38 genome
However, querying Ensembl and NCBI Gene
http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000012048
http://www.ncbi.nlm.nih.gov/gene/672
the gene is located at (note the difference in the end position)
Chromosome 17: 43,044,295-43,125,483 reverse strand
How is the inconsistency explained and how to extract an ENSEMBL/NCBI
conform annotation from the TxDb object?
(I am aware of biomaRt, but I want to explicitely use the Bioc annotation
functionality).
Thanks!
Ludwig
--
Dipl.-Bioinf. Ludwig Geistlinger
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München
Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de
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