[Bioc-sig-seq] makeTranscriptDbFromUCSC question

[Marc Carlson]

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
>
>
>
>       
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