Hi Dario,

The strand was converted to level type automatically, I will fix it as soon as I get access to the computer with SVN installed.

Meanwhile, please use the following code snippet, i.e., -1 as minus strand and 1 as positive strand. Thanks!

Best regards,

Julie

peaksT <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(1000, 2000, 3000), end = c(2000, 3000, 4000))

 featuresT <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(1500, 2500, 3500), end = c(2500, 3500, 4500), strand = c(-1))

 peaks <- RangedData(space = peaksT$chr, ranges = IRanges(start = peaksT$start, end = peaksT$end))
 features <- RangedData(space = featuresT$chr, strand = featuresT$strand, ranges = IRanges(start = featuresT$start, end = featuresT$end))

 annotatePeakInBatch(peaks, AnnotationData = features)
RangedData with 3 rows and 9 value columns across 1 space
          space       ranges |        peak      strand     feature start_position
    <character>    <IRanges> | <character> <character> <character>      <numeric>
1 1        chr1 [1000, 2000] |           1          -1           1           1500
2 1        chr1 [2000, 3000] |           2          -1           1           1500
3 2        chr1 [3000, 4000] |           3          -1           2           2500
    end_position insideFeature distancetoFeature shortestDistance fromOverlappingOrNearest
       <numeric>   <character>         <numeric>        <numeric>              <character>
1 1         2500    overlapEnd              1500              500             NearestStart
2 1         2500  overlapStart               500              500             NearestStart
3 2         3500  overlapStart               500              500             NearestStart


On 5/16/10 6:59 PM, "Dario Strbenac" <D.Strbenac@garvan.org.au> wrote:

Hello,

Here is my little test script :

peaksT <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(1000, 2000, 3000), end = c(2000, 3000, 4000), strand = c('+', '+', '+'))
featuresT <- data.frame(chr = c("chr1", "chr1", "chr1"), start = c(1500, 2500, 3500), end = c(2500, 3500, 4500), strand = c('-', '-', '-'))

peaks <- RangedData(space = peaksT$chr, strand = peaksT$strand, ranges = IRanges(start = peaksT$start, end = peaksT$end))
features <- RangedData(space = featuresT$chr, strand = featuresT$strand, ranges = IRanges(start = featuresT$start, end = featuresT$end))

annotatePeakInBatch(peaks, AnnotationData = features))

The sessionInfo is :

R version 2.11.0 (2010-04-22)
x86_64-pc-mingw32

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                       LC_TIME=English_Australia.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] ChIPpeakAnno_1.4.0                  limma_3.4.0                         org.Hs.eg.db_2.4.1                  GO.db_2.4.1                         RSQLite_0.9-0
 [6] DBI_0.2-5                           AnnotationDbi_1.10.1                BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.16.0                     GenomicRanges_1.0.1
[11] Biostrings_2.16.0                   IRanges_1.6.0                       multtest_2.4.0                      Biobase_2.8.0                       biomaRt_2.4.0

loaded via a namespace (and not attached):
[1] MASS_7.3-5      RCurl_1.3-1     splines_2.11.0  survival_2.35-8 tools_2.11.0    XML_2.8-1

Thanks,
       Dario.

---- Original message ----
>Date: Fri, 14 May 2010 07:38:20 -0400
>From: "Zhu, Julie" <Julie.Zhu@umassmed.edu>
>Subject: Re: [BioC] ChIPpeakAnno Critical Bug
>To: "D.Strbenac@garvan.org.au" <D.Strbenac@garvan.org.au>, "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch>
>
>   Hi Dario,
>
>   Could you please send your code snippets and session
>   info? Thanks!
>
>   Best regards,
>
>   Julie
>
>   On 5/14/10 1:48 AM, "Dario Strbenac"
>   <D.Strbenac@garvan.org.au> wrote:
>
>     Hello,
>
>     It seems that the annotatePeakInBatch function
>     completely ignores strand information :
>
>     > peaks
>     RangedData with 3 rows and 1 value column across 1
>     space
>             space       ranges |   strand
>       <character>    <IRanges> | <factor>
>     1        chr1 [1000, 2000] |        +
>     2        chr1 [2000, 3000] |        +
>     3        chr1 [3000, 4000] |        +
>     > features
>     RangedData with 3 rows and 1 value column across 1
>     space
>             space       ranges |   strand
>       <character>    <IRanges> | <factor>
>     1        chr1 [1500, 2500] |        -
>     2        chr1 [2500, 3500] |        -
>     3        chr1 [3500, 4500] |        -
>     > annotatePeakInBatch(peaks, AnnotationData =
>     features)
>     RangedData with 3 rows and 9 value columns across
>     1 space
>               space       ranges |        peak
>          strand     feature start_position
>     end_position insideFeature distancetoFeature
>     shortestDistance fromOverlappingOrNearest
>         <character>    <IRanges> | <character>
>     <character> <character>      <numeric>
>        <numeric>   <character>         <numeric>
>            <numeric>              <character>
>     1 1        chr1 [1000, 2000] |           1
>               1           1           1500
>             2500  overlapStart              -500
>                  500             NearestStart
>     2 1        chr1 [2000, 3000] |           2
>               1           1           1500
>             2500    overlapEnd               500
>                  500             NearestStart
>     3 2        chr1 [3000, 4000] |           3
>               1           2           2500
>             3500    overlapEnd               500
>                  500             NearestStart
>
>     Shouldn't get anything overlapping ...
>
>     --------------------------------------
>     Dario Strbenac
>     Research Assistant
>     Cancer Epigenetics
>     Garvan Institute of Medical Research
>     Darlinghurst NSW 2010
>     Australia
>
>     _______________________________________________
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