Hi Marc,
This seems like a good usecase to add to the vignette. Maybe we could
make it a formal task during the next stand up.
H.
Marc Carlson wrote:
Hi Joseph,
Here is a more generic approach you could take
##1st some setup for a toy example
library(GenomicFeatures)
txdb <- loadFeatures(system.file("extdata", "UCSC_knownGene_sample.sqlite",
package="GenomicFeatures"))
gr <- GRanges(seqnames = rep("chr1",2),
ranges = IRanges(start=c(500,10500),
end=c(10000,30000)),
strand = strand(rep("-",2)))
## You might want to just get a new ann by using transcripts() like this
ann = transcripts(txdb)
## Then you could add some padding to the upstream regions like so:
start(ann) = start(ann) - 10000
## and you can add to the end like this:
end(ann) = end(ann) + 10000
## Then you can use this modified annotation with findOverlaps
ol = findOverlaps(ann, gr)
## Then you could get the index of things that hit the subject
hits <- subjectHits(ol)
## and use that to see which things in gr are annotated.
gr[hits]
## Or use the queryHits to see what annotations go with your ranges
ann[unique(queryHits(ol))]
Does that help?
Marc
On 03/03/2010 02:28 PM, joseph wrote:
Hello
I am using transcriptsByRanges(txdb, gr) to annotate a set of reads with transcript and gene IDs
from txdb obtained with makeTranscriptDbFromUCSC(genome = "mm9", tablename =
"knownGene").
My question is how to make changes to the txdb to include 10 kb upstream of the transcription start site and 3 kb downstream of the end of the transcript.
Thanks
Joseph Dhahbi
[[alternative HTML version deleted]]
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
--
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: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
