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What is the recommended method for saving/loading a TxDb object?
> example(makeTxDb) mkTxDb> transcripts <- data.frame( mkTxDb+ tx_id=1:3, mkTxDb+ tx_chrom="chr1", mkTxDb+ tx_strand=c("-", "+", "+"), mkTxDb+ tx_start=c(1, 2001, 2001), mkTxDb+ tx_end=c(999, 2199, 2199)) mkTxDb> splicings <- data.frame( mkTxDb+ tx_id=c(1L, 2L, 2L, 2L, 3L, 3L), mkTxDb+ exon_rank=c(1, 1, 2, 3, 1, 2), mkTxDb+ exon_start=c(1, 2001, 2101, 2131, 2001, 2131), mkTxDb+ exon_end=c(999, 2085, 2144, 2199, 2085, 2199), mkTxDb+ cds_start=c(1, 2022, 2101, 2131, NA, NA), mkTxDb+ cds_end=c(999, 2085, 2144, 2193, NA, NA)) mkTxDb> txdb <- makeTxDb(transcripts, splicings) Warning message: In .normarg_makeTxDb_chrominfo(chrominfo, transcripts$tx_chrom, : chromosome lengths and circularity flags are not available for this TxDb object > txdb TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # transcript_nrow: 3 # exon_nrow: 4 # cds_nrow: 4 # Db created by: GenomicFeatures package from Bioconductor # Creation time: 2015-06-09 07:13:11 -0700 (Tue, 09 Jun 2015) # GenomicFeatures version at creation time: 1.20.1 # RSQLite version at creation time: 1.0.0 # DBSCHEMAVERSION: 1.1 > save(txdb, file = "tmp.Rdata") > rm(txdb) > load("tmp.Rdata") > txdb TxDb object: Error in sqliteSendQuery(con, statement, bind.data) : expired SQLiteConnection
Nice! Thanks Martin.