Thanks! Kasper, it is good to know that. I am using UCSC annotation :)

Sabrina

On Tue, Mar 2, 2010 at 9:27 AM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> One thing you want to be careful with when you do stuff like this, is
> that the annotation matches up _exactly_ with the genome you are
> using.  This really bit me in S. cerevisiae.  Essentially even a small
> indel will make everything out of phase.  And you really need to watch
> out for different versions of the genome.  Sometimes extra stuff gets
> resolved at the end of the chromosomes.
>
> In this case it seems you are using UCSC annotation and BSgenome so it
> should work.  But I urge you to double check.  This is something that
> can be very hard to track down.
>
> Kasper
>
> On Tue, Mar 2, 2010 at 9:21 AM, sabrina s <sabrina.shao@gmail.com> wrote:
> > Hi, Michael:
> >
> > See bellow:
> >
> >
> > Error in IRanges:::.normargSEW(start, "start") :
> >  'start' must be a vector of integers
> >> sessionInfo()
> > R version 2.10.0 (2009-10-26)
> > i386-pc-mingw32
> >
> > locale:
> > [1] LC_COLLATE=English_United States.1252
> > [2] LC_CTYPE=English_United States.1252
> > [3] LC_MONETARY=English_United States.1252
> > [4] LC_NUMERIC=C
> > [5] LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 BSgenome_1.14.2
> > [3] Biostrings_2.14.5                  rtracklayer_1.6.0
> > [5] RCurl_1.3-1                        bitops_1.0-4.1
> > [7] IRanges_1.4.10
> >
> > loaded via a namespace (and not attached):
> > [1] Biobase_2.6.0 XML_2.6-0
> >
> >
> > Thanks!
> >
> > Sabrina
> >
> >
> > On Tue, Mar 2, 2010 at 8:49 AM, Michael Lawrence
> > <lawrence.michael@gene.com>wrote:
> >
> >> Could you paste your sessionInfo() output please?
> >>
> >>
> >> On Mon, Mar 1, 2010 at 7:37 PM, sabrina s <sabrina.shao@gmail.com>
> wrote:
> >>
> >>> Hi, Michael:
> >>>
> >>> I tried as you suggested, but I had the following error:
> >>>
> >>> Error in IRanges:::.normargSEW(start, "start") :
> >>>   'start' must be a vector of integers
> >>>
> >>> my testTrack looks like this:
> >>>
> >>> RangedData with 76 rows and...
> >>>          space                 ranges |        strand
> >>>    <character>              <IRanges> |  <factor>
> >>> 1         chr1 [137159091, 137159290] |        -
> >>> 2         chr1 [155302742, 155302941] |       -
> >>> etc
> >>>
> >>> Any suggestions? Thanks!
> >>>
> >>> Sabrina
> >>>
> >>>
> >>> On Mon, Mar 1, 2010 at 6:02 PM, Michael Lawrence <
> >>> lawrence.michael@gene.com> wrote:
> >>>
> >>>>
> >>>>
> >>>> On Mon, Mar 1, 2010 at 1:02 PM, sabrina s <sabrina.shao@gmail.com
> >wrote:
> >>>>
> >>>>> Hi, Steve:
> >>>>> I am trying to get it worked without separating the chromosomes. I
> used
> >>>>> the
> >>>>> following code:
> >>>>> seqQuery<-data.frame(
> >>>>>        chr=currCoorList$chr,
> >>>>>    start=currCoorList$starts,
> >>>>>    end=currCoorList$ends,
> >>>>>    strand=currCoorList$strand)
> >>>>>    mySeq<- getSeq(Mmusculus, seqQuery$chr,
> >>>>>         start=seqQuery$start, end=seqQuery$end,
> >>>>>            strand=seqQuery$strand )
> >>>>>
> >>>>>
> >>>>> But then I got an error:
> >>>>> Error in reverseComplement(DNAStringSet(seqs[ii])) :
> >>>>>  could not find function "copy"
> >>>>>
> >>>>
> >>>> Did I miss some depending package?
> >>>>>
> >>>>>
> >>>> Don't know what's up with that, but you don't need to use a data.frame
> >>>> there. You already had a RangedData above, just pass that to getSeq,
> i.e.
> >>>>
> >>>> getSeq(Mmusculus, testTrack)
> >>>>
> >>>>  Sabrina
> >>>>>
> >>>>> On Mon, Mar 1, 2010 at 2:31 PM, Steve Lianoglou <
> >>>>> mailinglist.honeypot@gmail.com> wrote:
> >>>>>
> >>>>> > Hi Sabrina,
> >>>>> >
> >>>>> > On Mon, Mar 1, 2010 at 2:04 PM, sabrina s <sabrina.shao@gmail.com>
> >>>>> wrote:
> >>>>> > > Hi,all:
> >>>>> > > I have a long list of coordinates, which was created by the
> >>>>> following
> >>>>> > code:
> >>>>> > > testIranges<- IRanges(start=currCoorList $starts,
> >>>>> > >        end=currCoorLis$ends)
> >>>>> > >
> >>>>> > >   testTrack<-GenomicData(testIranges,chrom=currCoorList$chr,
> >>>>> > >        strand=currCoorList$strand,genome="mm9")
> >>>>> > >
> >>>>> > > I could then export the testTrack into .bed file and upload in
> the
> >>>>> UCSC
> >>>>> > > genome browser and get the sequences of the listed coordinate
> >>>>> > > But I was thinking if there is a function from rtracklayer to
> >>>>> retrieve
> >>>>> > > sequence directly.
> >>>>> >
> >>>>> > If you're trying to get coordinates from some reference genome, you
> >>>>> > can use the BSgenome.*.* packages and skip rtracklayer + internet
> >>>>> > queries entirely.
> >>>>> >
> >>>>> > For instance, say I have an IRanges object `r1` which is a set of
> >>>>> > intervals on chromosome 1 from hg18 that I want sequence
> information
> >>>>> > for, I could do it like this:
> >>>>> >
> >>>>> > R> r1
> >>>>> > IRanges of length 589
> >>>>> >        start      end width
> >>>>> > [1]   18016124 18016155    32
> >>>>> > [2]   18020749 18020780    32
> >>>>> > [3]   18024599 18024630    32
> >>>>> > [4]   18024830 18024861    32
> >>>>> > [5]   18051985 18052016    32
> >>>>> > [6]   18064760 18064791    32
> >>>>> > [7]   18088145 18088176    32
> >>>>> > [8]   18088200 18088231    32
> >>>>> > [9]   18110085 18110116    32
> >>>>> > ...
> >>>>> >
> >>>>> > R> library(BSgenome.Hsapiens.UCSC.hg18)
> >>>>> > R> chr1 <- unmasked(HSapiens$chr1)
> >>>>> > R> myseqs <- Views(chr1, start=start(r1), end=end(r1))
> >>>>> > R> myseqs
> >>>>> >  Views on a 247249719-letter DNAString subject
> >>>>> > subject:
> >>>>> >
> >>>>>
> TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> >>>>> > views:
> >>>>> >        start      end width
> >>>>> > [1] 18016124 18016155    32 [GTTTTTTGTTTTGTTTTGTTTTTTGTTTTTTA]
> >>>>> > [2] 18020749 18020780    32 [CGCCTAGTCTGGAGTGCAGTGGCACAATCTTG]
> >>>>> > [3] 18024599 18024630    32 [TCTCACCTCTTCACCGAAGTGGTCTTCTGAAC]
> >>>>> > [4] 18024830 18024861    32 [GAATTCTCCCTCGTTGCAGATCCTGTTTGAGT]
> >>>>> > [5] 18051985 18052016    32 [TTATTTTTTTTGAGGAAGAGTCTTGCTCTGTC]
> >>>>> > [6] 18064760 18064791    32 [GTGGGAGGATCGCTTGAGCCCTGGAGGTTGGG]
> >>>>> > [7] 18088145 18088176    32 [ATCATGGTGGGAGATGAAAGGCACTTCTTACA]
> >>>>> > [8] 18088200 18088231    32 [GAAGAAGCAAAAGCGGAAACCCCTGCTAAACC]
> >>>>> > [9] 18110085 18110116    32 [GGATCATGAGTTCAAGAGTTCGAGACCAGCCT]
> >>>>> > [10] 18118454 18118485    32 [TGTTGCCTAGGCTGGTCTCAAACTCCTGCCCT]
> >>>>> > ...
> >>>>> >
> >>>>> > calling "as.character" on the myseqs object will give you the
> sequence
> >>>>> > as a character vector.
> >>>>> >
> >>>>> > Does that get you what you're after?
> >>>>> > -steve
> >>>>> >
> >>>>> > --
> >>>>> > Steve Lianoglou
> >>>>> > Graduate Student: Computational Systems Biology
> >>>>> >  | Memorial Sloan-Kettering Cancer Center
> >>>>> >  | Weill Medical College of Cornell University
> >>>>> > Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
> <http://cbio.mskcc.org/%7Elianos/contact>
> >>>>> <http://cbio.mskcc.org/%7Elianos/contact>
> >>>>> >
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Sabrina
> >>>>>
> >>>>>        [[alternative HTML version deleted]]
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioconductor mailing list
> >>>>> Bioconductor@stat.math.ethz.ch
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>> Search the archives:
> >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>>>
> >>>>
> >>>>
> >>>
> >>>
> >>> --
> >>> Sabrina
> >>>
> >>
> >>
> >
> >
> > --
> > Sabrina
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>



-- 
Sabrina

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