Hello****

I am trying to use rtracklayer and specifically UCSCTableQuery to retrieve
information from UCSC tables but I want to retrieve the information  only
on certain genomic segments. ****

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In the following example I try to create a UCSCTableQuery that will return
A GRanges of the  tRNAs in a set of given ranges, defined by a GRanges
object . Specifically, I am interested in all the tRNAs that fall within
CpG islands.    ****

In order to accomplish this, I first created a GRanges object (islandshg19)
derived from UCSC CpG islands track:****

session <- browserSession()****

genome(session)<-"hg19"****

query <- ucscTableQuery(session, "CpG Islands")# define track****

islandshg19<-track(query, asRangedData=FALSE)# creates a grange of all CpG
island****

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Next I try to use a UCSCTableQuery with the range defined as the island
GRanges:****

query <- ucscTableQuery(session, "tRNAs", range= islandshg19,
table="tRNAs", names=NULL)****

this produced the error:****

Error in normGenomeRange(range, x) : ****

  'range' must contain ranges on a single chromosome****

 ****

I then attempted to run the query after creating a subset of CpG islands on
chromosome 1 (chr1):****

query <- ucscTableQuery(session, "tRNAs", range=chr1, table="tRNAs",
names=NULL)****

chr1tRNAs<-track(query, asRangedData=FALSE)# creates a grange****

This indeed produced a UCSCTableQuery object, however, the qurey returned
tRNAs not overlapped by any CpG island included in the chr1 GRAnges.  it
seems that the range the query returns is the entire portion of chr1
between the smallest and largest coordiantes in the chr1 object.****

****

I have two questions:****

a) how  to set the query so that it will return only those tRNAs
overlapping CpG islands? ****

b) is it possible to use UCSCTableQuery to this end on GRanges located on
more than one chromosome?****

****

Thanks in advance****

Dolev Rahat****

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