Hi,
I was exploring the rhesus macaque package:
> TxDb.Mmulatta.UCSC.rheMac8.refGene
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC rheMac8 refGene
# Organism: Macaca mulatta
# Taxonomy ID: 9544
# miRBase build ID: NA
# Genome: NA
# transcript_nrow: 6378
# exon_nrow: 46356
# cds_nrow: 43281
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-10-02 12:20:15 -0400 (Mon, 02 Oct 2017)
# GenomicFeatures version at creation time: 1.29.11
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1
# Resource URL: http://genome.ucsc.edu/cgi-bin/hgTables
Does "# transcript_nrow: 6378" mean that there is information for only, at most, 6378 genes in this package. Sorry, not familiar with this organism, but doesn't 6378 genes seem a bit on the small size considering it is for the entire genome?
Or have I mis-understood something?
many thanks!