HI Are there plans to release hg19 of GenomicFeatures.Hsapiens.UCSC soon? We would greatly appreciate it. Thanks -burak -- Burak Kutlu, PhD. Research Scientist Hood Lab Institute for Systems Biology

Hi Are there plans to release the hg19 version of GenomicFeatures.Hsapiens.UCSC soon? Thanks -burak

Hi Burak, Burak Kutlu wrote: > HI > Are there plans to release hg19 of GenomicFeatures.Hsapiens.UCSC soon? > We would greatly appreciate it. The GenomicFeatures *data* packages are deprecated. Use the GenomicFeatures *software* package (make sure you use the current BioC release, i.e. BioC 2.6, it requires R-2.11) to do: txdb <- makeTranscriptDbFromUCSC("hg19") > txdb TranscriptDb object: | Db type: TranscriptDb | Data source: UCSC | Genome: hg19 | UCSC Table: knownGene | Type of Gene ID: Entrez Gene ID | Full dataset: yes | transcript_nrow: 77614 | exon_nrow: 281605 | cds_nrow: 236664 | Db created by: GenomicFeatures package from Bioconductor | Creation time: 2010-04-24 14:22:14 -0700 (Sat, 24 Apr 2010) | GenomicFeatures version at creation time: 1.0.0 | RSQLite version at creation time: 0.8-4 Then have a look at the vignettes in GenomicFeatures to learn how to query 'txdb' (a TranscriptDb object). For example, to extract the exon structure of all the transcripts (or, said otherwise, to extract the exons grouped by transcript): > exbytx <- exonsBy(txdb, "tx") > exbytx GRangesList of length 77614 $1 GRanges with 3 ranges and 3 elementMetadata values seqnames ranges strand | exon_id exon_name exon_rank <rle> <iranges> <rle> | <integer> <character> <integer> [1] chr1 [11874, 12227] + | 1 NA 1 [2] chr1 [12613, 12721] + | 2 NA 2 [3] chr1 [13221, 14409] + | 3 NA 3 $2 GRanges with 3 ranges and 3 elementMetadata values seqnames ranges strand | exon_id exon_name exon_rank <rle> <iranges> <rle> | <integer> <character> <integer> [1] chr1 [11874, 12227] + | 1 NA 1 [2] chr1 [12595, 12721] + | 4 NA 2 [3] chr1 [13403, 14409] + | 5 NA 3 $3 GRanges with 3 ranges and 3 elementMetadata values seqnames ranges strand | exon_id exon_name exon_rank <rle> <iranges> <rle> | <integer> <character> <integer> [1] chr1 [11874, 12227] + | 1 NA 1 [2] chr1 [12646, 12697] + | 6 NA 2 [3] chr1 [13221, 14409] + | 3 NA 3 ... <77611 more elements> seqlengths chr1 chr2 ... chr18_gl000207_random 249250621 243199373 ... 4262 Cheers, H. > Thanks > -burak > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319