[BioC] inconsistency between GRangesList and transcriptDB object.

[zhenjiang xu]

Hi,

There are 6717 transcripts read into txdb but why GRangesList is only
6550 long? Thanks

>   txdb <- makeTranscriptDbFromUCSC(genome="sacCer2", tablename="sgdGene")
Download the sgdGene table ... OK
Download the sgdIsoforms table ... OK
Download the sgdCanonical table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
>   tx_by_gene <- transcriptsBy(txdb,'gene')
> txdb
TranscriptDb object:
| Db type: TranscriptDb
| Data source: UCSC
| Genome: sacCer2
| UCSC Table: sgdGene
| Type of Gene ID: ID of canonical transcript in cluster
| Full dataset: yes
| transcript_nrow: 6717
| exon_nrow: 7083
| cds_nrow: 7061
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2011-04-20 11:20:56 -0400 (Wed, 20 Apr 2011)
| GenomicFeatures version at creation time: 1.2.3
| RSQLite version at creation time: 0.9-4
| DBSCHEMAVERSION: 1.0
> tx_by_gene
GRangesList of length 6550
$Q0010
GRanges with 2 ranges and 2 elementMetadata values
    seqnames       ranges strand |     tx_id     tx_name
       <Rle>    <IRanges>  <Rle> | <integer> <character>
[1]     chrM [3952, 4338]      + |       122       Q0010
[2]     chrM [4254, 4415]      + |       123       Q0017

$Q0032
GRanges with 1 range and 2 elementMetadata values
    seqnames         ranges strand |     tx_id     tx_name
       <Rle>      <IRanges>  <Rle> | <integer> <character>
[1]     chrM [11667, 11957]      + |       124       Q0032


-- 
Best,
Zhenjiang