Hi Michael, On 07/08/2014 12:11 PM, Michael Love wrote:
The recent TranscriptDb thread reminded me of a question: are there plans (or am I missing the function) to easily get a TranscriptDb out of the AnnotationHub objects? It would be great to have a preprocessed Ensembl txdb like we have for UCSC.
I think the 1st thing we should do is have a makeTranscriptDbFromGRanges() function. It should not be too hard
because we already have the code :) Marc wrote it. But it's currently part of the makeTranscriptDbFromGFF() function. Roughly speaking this function does 2 things: (1) import the GFF or GTF file as a GRanges object, then (2) turn that GRanges object into a TranscriptDb object. So we should move the code that does (2) into a separate function, the makeTranscriptDbFromGRanges() function, and have makeTranscriptDbFromGFF() call it internally. Then you could call makeTranscriptDbFromGRanges() on any of these GFF- or GTF-based GRanges objects you get from AnnotationHub. We'll work on this soon and announce here when it becomes available. Cheers, H.
ah <- AnnotationHub() gr <- ah$ensembl.release.73.gtf.homo_sapiens.Homo_sapiens.GRCh37.73.gtf_0.0.1.RData grGRanges with 2268089 ranges and 12 metadata columns: seqnames ranges strand | source <Rle> <IRanges> <Rle> | <factor> [1] 1 [11869, 12227] + | processed_transcript [2] 1 [12613, 12721] + | processed_transcript [3] 1 [13221, 14409] + | processed_transcript [4] 1 [11872, 12227] + | unprocessed_pseudogene [5] 1 [12613, 12721] + | unprocessed_pseudogene ... ... ... ... ... ... [2268085] MT [14747, 15887] + | protein_coding [2268086] MT [14747, 15887] + | protein_coding [2268087] MT [14747, 14749] + | protein_coding [2268088] MT [15888, 15953] + | Mt_tRNA [2268089] MT [15956, 16023] - | Mt_tRNA type score phase gene_id transcript_id <factor> <numeric> <integer> <character> <character> [1] exon <NA> <NA> ENSG00000223972 ENST00000456328 [2] exon <NA> <NA> ENSG00000223972 ENST00000456328 [3] exon <NA> <NA> ENSG00000223972 ENST00000456328 [4] exon <NA> <NA> ENSG00000223972 ENST00000515242 [5] exon <NA> <NA> ENSG00000223972 ENST00000515242 ... ... ... ... ... ... [2268085] exon <NA> <NA> ENSG00000198727 ENST00000361789 [2268086] CDS <NA> 0 ENSG00000198727 ENST00000361789 [2268087] start_codon <NA> 0 ENSG00000198727 ENST00000361789 [2268088] exon <NA> <NA> ENSG00000210195 ENST00000387460 [2268089] exon <NA> <NA> ENSG00000210196 ENST00000387461 exon_number gene_name gene_biotype transcript_name <numeric> <character> <character> <character> [1] 1 DDX11L1 pseudogene DDX11L1-002 [2] 2 DDX11L1 pseudogene DDX11L1-002 [3] 3 DDX11L1 pseudogene DDX11L1-002 [4] 1 DDX11L1 pseudogene DDX11L1-201 [5] 2 DDX11L1 pseudogene DDX11L1-201 ... ... ... ... ... [2268085] 1 MT-CYB protein_coding MT-CYB-201 [2268086] 1 MT-CYB protein_coding MT-CYB-201 [2268087] 1 MT-CYB protein_coding MT-CYB-201 [2268088] 1 MT-TT Mt_tRNA MT-TT-201 [2268089] 1 MT-TP Mt_tRNA MT-TP-201 exon_id protein_id <character> <character> [1] ENSE00002234944 <NA> [2] ENSE00003582793 <NA> [3] ENSE00002312635 <NA> [4] ENSE00002234632 <NA> [5] ENSE00003608237 <NA> ... ... ... [2268085] ENSE00001436074 <NA> [2268086] <NA> ENSP00000354554 [2268087] <NA> <NA> [2268088] ENSE00001544475 <NA> [2268089] ENSE00001544473 <NA> --- seqlengths: 1 2 ... MT NA NA ... NA _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
