Hi Dario,

Since this is a feature request, I will add it to the dev branch for you to install.

Best,

Julie


On 5/16/10 7:04 PM, "Dario Strbenac" <D.Strbenac@garvan.org.au> wrote:

Not quite. I mean that midpoint to midpoint distance would be good when the feature didn't have a strand. If the feature does have strand information, then it'd be nice to have midpoint of peak to start (start for + strand, end for - strand) of feature.

Thanks,
       Dario.

---- Original message ----
>Date: Fri, 14 May 2010 07:43:38 -0400
>From: "Zhu, Julie" <Julie.Zhu@umassmed.edu>
>Subject: Re: ChIPpeakAnno Strandedness and distance calculation
>To: "D.Strbenac@garvan.org.au" <D.Strbenac@garvan.org.au>
>Cc: "bioconductor" <bioconductor@stat.math.ethz.ch>
>
>   Hi Dario,
>
>   Thanks for the clarification! So you still want the
>   nearest feature and  insideFeature column to be
>   calculated using start (+ strand) and end (-
>   strand). You only need an extra column with distance
>   from midpoint to midpoint to be included?
>
>   Best regards,
>
>   Julie
>
>   On 5/14/10 12:20 AM, "Dario Strbenac"
>   <D.Strbenac@garvan.org.au> wrote:
>
>     Oh, actually I thought of a problem with making
>     start = midpoint. If you modify the start position
>     to be the average, then you might get the wrong
>     values in insideFeature column.
>
>     e.g.
>
>     Peak
>     Real coordinates
>     --------------------
>     chr  | start | end  |
>     -------------------
>     chr1 | 5000  | 5500 |
>
>     Peak
>     modified coordinates (start is midpoint)
>     --------------------
>     chr  | start | end  |
>     -------------------
>     chr1 | 5250  | 5500 |
>
>     A gene
>     -----------------------------
>     chr  | start | end | strand |
>     -----------------------------
>     chr1 | 1000  | 5100 |    -  |
>
>     So, instead of being 'overlapStart', it is called
>     as 'upstream'.
>
>     It would be good if the package worked out an
>     extra column for the tables, called 'position' and
>     used the position for the distances, and the real
>     start and end positions for the overlapping.
>
>     e.g. Something like this
>
>     if("strand" %in% colnames(table))
>     {
>       table$position = ifelse(table$strand == '+',
>     table$start, table$end)
>     } else {
>       table$position = round((table$start + table$end)
>     / 2)
>     }
>
>     - Dario.
>     ---- Original message ----
>     >Date: Thu, 13 May 2010 22:40:46 -0400
>     >From: "Zhu, Julie" <Julie.Zhu@umassmed.edu>
>     >Subject: Re: ChIPpeakAnno Strandedness and
>     distance calculation
>     >To: "D.Strbenac@garvan.org.au"
>     <D.Strbenac@garvan.org.au>
>     >Cc: "bioconductor"
>     <bioconductor@stat.math.ethz.ch>
>     >
>     >Hi Dario,
>     >
>     >You can create the annotation with strand =
>     c("+"). For example,
>     >
>     >AnnotationRangedData = RangedData(IRanges(start =
>     c(967659, 2010898,
>     >2496700, 3075866,
>     >+ 3123260), end = c(967869, 2011108, 2496920,
>     3076166, 3123470), names =
>     >c("t1",
>     >+ "t2", "t3", "t4", "t5")), space = c("1", "2",
>     "3", "1", "2"), strand
>     >=c("+"))
>     >
>     >Please take a look at the examples given on the
>     paper just published on BMC
>     >Bioinformatics
>     >http://www.biomedcentral.com/1471-2105/11/237. In
>     case you could not open
>     >the link, I also attached the pdf file.
>     >
>     >Regarding your other question about distance
>     calculation, I suggest to
>     >create your AnnotationRangedData and
>     PeakRangedData with start=midpoint to
>     >get the distance between midpoints.  The distance
>     is calculated differently
>     >for features in plus strand and minus strand. For
>     example, to calculate the
>     >distance between peak and TSS, the distance is
>     calculated as the distance
>     >between the start of the binding site and the
>     TSS, which is the gene start
>     >for genes located on the forward strand and the
>     gene end for genes located
>     >on the reverse strand. Therefore, adding another
>     parameter would mean to
>     >overwrite the way how the distance is calculated
>     based on strandedness.
>     >After you tried the above suggested way and still
>     prefer having a new
>     >parameter, I will be happy to add it to the next
>     release.
>     >
>     >Best regards,
>     >
>     >Julie
>     >
>     >
>     >*******************************************
>     >Lihua Julie Zhu, Ph.D
>     >Research Associate Professor
>     >Program in Gene Function and Expression
>     >Program in Molecular Medicine
>     >University of Massachusetts Medical School
>     >364 Plantation Street, Room 613
>     >Worcester, MA 01605
>     >508-856-5256
>     >http://www.umassmed.edu/pgfe/faculty/zhu.cfm
>     >
>     >
>     >
>     >
>     >
>     >On 5/13/10 9:00 PM, "Dario Strbenac"
>     <D.Strbenac@garvan.org.au> wrote:
>     >
>     >> Hello again,
>     >>
>     >> Just one more question. When we are looking at
>     DNA methtylation, we don't have
>     >> the strand of the peak (because the reverse
>     complement of CG is CG). It seems
>     >> that it might not be possible to do this with
>     ChipPeakAnno ?
>     >>
>     >> e.g.
>     >>
>     >>> > head(peaksT)
>     >>     chr     start       end
>     >> 1 chr13  83351701  83352000
>     >> 2 chr13  83351401  83351700
>     >> 3 chr20  25011901  25012200
>     >> 4 chr13  83352001  83352300
>     >> 5  chr8 143402101 143402400
>     >> 6  chr2 238246801 238247100
>     >>
>     >>> > head(featTable)
>     >>      name  chr strand  start    end
>     >> 1 7896759 chr1      + 781253 783614
>     >> 2 7896761 chr1      + 850983 869824
>     >> 3 7896779 chr1      + 885829 890958
>     >> 4 7896798 chr1      + 891739 900345
>     >> 5 7896817 chr1      + 938709 939782
>     >> 6 7896822 chr1      + 945365 981355
>     >>
>     >> Also, sometimes our feature table is a table of
>     CpG islands, which don't have
>     >> a strand associated with them.
>     >>
>     >> e.g.
>     >>
>     >>> > head(featTable2)
>     >>    chr  start    end CpG Island Name
>     >> 1 chr1  18598  19673        CpG:_116
>     >> 2 chr1 124987 125426         CpG:_30
>     >> 3 chr1 317653 318092         CpG:_29
>     >> 4 chr1 427014 428027         CpG:_84
>     >> 5 chr1 439136 440407         CpG:_99
>     >> 6 chr1 523082 523977         CpG:_94
>     >>
>     >> Is it possible to do this annotation with
>     ChipPeakAnno ? Currently, the
>     >> annotatePeakInBatch function gives me an error
>     when I don't give it strand
>     >> information when I create my RangedData object.
>     >>
>     >> Thanks,
>     >>        Dario.
>     >>
>     >> --------------------------------------
>     >> Dario Strbenac
>     >> Research Assistant
>     >> Cancer Epigenetics
>     >> Garvan Institute of Medical Research
>     >> Darlinghurst NSW 2010
>     >> Australia
>     >>
>     >>
>     >
>     >On 5/13/10 8:10 PM, "Dario Strbenac"
>     <D.Strbenac@garvan.org.au> wrote:
>     >
>     >> Hello,
>     >>
>     >> Firstly, thank you for making this package. It
>     seems so useful ! We were
>     >> thinking of writing something like this
>     ourselves, until I saw your package,
>     >> because we do a lot of ChIP-Seq here.
>     >>
>     >> I just have a small feature request. In your
>     distance calculation, you do
>     >> start of peak - start of feature. Would it be
>     possible to allow the user to
>     >> choose if they want the distance calculation to
>     use the start or the middle of
>     >> the feature (and also for the peak) ? This is
>     because we do a lot of
>     >> methylation studies, and for CpG island
>     features, we like to use the midpoint
>     >> as the position of our feature. It would also
>     be nice to be able to use the
>     >> midpoint of the peak as the peak's position,
>     since this is usually where the
>     >> signal is strongest.
>     >>
>     >> Thanks,
>     >>       Dario.
>     >>
>     >> --------------------------------------
>     >> Dario Strbenac
>     >> Research Assistant
>     >> Cancer Epigenetics
>     >> Garvan Institute of Medical Research
>     >> Darlinghurst NSW 2010
>     >> Australia
>     >
>     >
>
>     --------------------------------------
>     Dario Strbenac
>     Research Assistant
>     Cancer Epigenetics
>     Garvan Institute of Medical Research
>     Darlinghurst NSW 2010
>     Australia



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