conradstack/bsgenome.tcacao

R packages containing cacao reference genomes in bioconductor (BSgenome) format.

bsgenome.tcacao's Issues

TxDb object(s) should contain TXSOURCE column

This is missing from the marina 1-6 txdb package. It should be included in future updates.

library(TxDb.Tcacao.Geneious.pub3i) txdb = TxDb.Tcacao.Geneious.pub3i columns(txdb)

Warnings when using txdb object

selcols = c("TXID","TXNAME", "TXSTART","TXEND", "TXMODELNAME","TXQUALCLASS","TXTYPE") # columns to pull out for each gene model (GENEID) entry
Warning messages:
1: In installClassMethod(value, self, field, selfEnv, thisClass) :
method .objectPackage from class TxDb was not processed into a class method until being installed. Possible corruption of the methods in the class.
2: In installClassMethod(value, self, field, selfEnv, thisClass) :
method .objectParent from class TxDb was not processed into a class method until being installed. Possible corruption of the methods in the class.
txinfo = select(txdb,

•    keys=models$Gene.Name.V1.1, 
  

•    keytype="GENEID",
  

•    columns=selcols)