Hi,

I am using the findOverlapsOfPeaks function from the ChIPpeakAnno_3.2.0 package.

Is there a possibility to keep the metadata of the GRanges objects used for the overlap? Would be nice to have it in the output (peaklist GRanges).

Or to at least keep the peak names from the input. For me it seems like findOverlapsOfPeaks is using the name of the GRanges + number for the peak names in the output peaklist.

GRanges1 peak=protA_antibody_1212
GRanges2 peak=protB_antibody_5894
names used in peaklist GRanges1///GRanges2:   GRanges1__1, GRanges2__1
would like to have: protA_antibody_1212, protB_antibody_5894

Thanks for your help!
Dagmar

Hi Hari,

Please update your R into 3.2.0 or above.

findOverlapsOfPeaks function is introduced in ChIPpeakAnno v3.2.0 (happened to be same as R version) or above.

You may interested in ChIPseeker, http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btv145

Hi Dagmar,

It is very interesting. It should be designed to show the peak names in the output of peaklist. If there are duplicated names or NA names, it will convert to peak number. I am not sure I fully understand your case. If you got peak names in GRanges1 and GRanges2, but not got peak names in overlapping peaks, this should be a bug. If this is the case, could you kindly send me your data and the code to repeat that? Thank you.

> library(ChIPpeakAnno)
> packageVersion("ChIPpeakAnno")
[1] ‘3.2.0’
> bed <- system.file("extdata", "MACS_output.bed", package="ChIPpeakAnno")
> gr1 <- toGRanges(bed, format="BED", header=FALSE)
> gff <- system.file("extdata", "GFF_peaks.gff", package="ChIPpeakAnno")
> gr2 <- toGRanges(gff, format="GFF", header=FALSE, skip=3)
> head(gr1)
GRanges object with 6 ranges and 1 metadata column:
              seqnames           ranges strand |     score
                 <Rle>        <IRanges>  <Rle> | <numeric>
  MACS_peak_1     chr1 [ 28341,  29610]      * |    160.81
  MACS_peak_2     chr1 [ 90821,  91234]      * |    133.12
  MACS_peak_3     chr1 [134974, 135538]      * |    138.99
  MACS_peak_4     chr1 [136331, 137068]      * |    106.17
  MACS_peak_5     chr1 [137277, 137847]      * |     124.9
  MACS_peak_6     chr1 [326732, 327221]      * |    190.74
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> head(gr2)
GRanges object with 6 ranges and 4 metadata columns:
           seqnames           ranges strand |   source     score    frame     group
              <Rle>        <IRanges>  <Rle> | <factor> <integer> <factor>  <factor>
  region_0     chr1 [713893, 714747]      + |  bed2gff         0        . region_0;
  region_1     chr1 [715023, 715578]      + |  bed2gff         0        . region_1;
  region_2     chr1 [724851, 725445]      + |  bed2gff         0        . region_2;
  region_3     chr1 [839467, 840090]      + |  bed2gff         0        . region_3;
  region_4     chr1 [856361, 856999]      + |  bed2gff         0        . region_4;
  region_5     chr1 [859315, 859903]      + |  bed2gff         0        . region_5;
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> head(peaklist[[3]])
GRanges object with 6 ranges and 1 metadata column:
      seqnames           ranges strand |                                     peakNames
         <Rle>        <IRanges>  <Rle> |                               <CharacterList>
  [1]     chr1 [713791, 715578]      * | gr1__MACS_peak_13,gr2__region_0,gr2__region_1
  [2]     chr1 [724851, 727191]      * |               gr2__region_2,gr1__MACS_peak_14
  [3]     chr1 [839467, 840090]      * |               gr1__MACS_peak_16,gr2__region_3
  [4]     chr1 [856361, 856999]      * |               gr1__MACS_peak_17,gr2__region_4
  [5]     chr1 [859315, 860144]      * |               gr2__region_5,gr1__MACS_peak_18
  [6]     chr1 [870970, 871568]      * |               gr2__region_7,gr1__MACS_peak_19
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

> ol <- findOverlapsOfPeaks(gr1, gr2)
> peaklist <- ol$peaklist
> names(peaklist)
[1] "gr2"       "gr1"       "gr1///gr2"
> head(peaklist[[1]])
GRanges object with 6 ranges and 1 metadata column:
      seqnames             ranges strand |       peakNames
         <Rle>          <IRanges>  <Rle> | <CharacterList>
  [1]     chr1 [ 860248,  860833]      + |   gr2__region_6
  [2]     chr1 [ 905647,  906230]      + |  gr2__region_12
  [3]     chr1 [ 908528,  909096]      + |  gr2__region_13
  [4]     chr1 [ 918145,  918733]      + |  gr2__region_16
  [5]     chr1 [ 986902,  987370]      + |  gr2__region_23
  [6]     chr1 [1004125, 1004714]      + |  gr2__region_26
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

I am facing a weird problem with ChIPpeakAnno. I am  to able to fine the function findOverlapsOfPeaks. I get the following:

> findOverlapsOfPeaks
Error: object 'findOverlapsOfPeaks' not found

However, other functions like annotatePeakInBatch can be found.

Any idea what could be wrong. Thanks for your help.

> R.Version()
$platform
[1] "x86_64-apple-darwin10.8.0"

$arch
[1] "x86_64"

$os
[1] "darwin10.8.0"

$system
[1] "x86_64, darwin10.8.0"

$status
[1] ""

$major
[1] "3"

$minor
[1] "1.3"

$year
[1] "2015"

$month
[1] "03"

$day
[1] "09"

$`svn rev`
[1] "67962"

$language
[1] "R"

$version.string
[1] "R version 3.1.3 (2015-03-09)"

$nickname
[1] "Smooth Sidewalk"

Hi Jianhong, Thanks for your message. It works now. Earlier I had a problem with R3.2 in that it could not find BiocParallel, and I could not install it. Had to restart R and reinstall Bioconductor, ChIPpeakAnno, BiocParallel.... it works now.

Thanks.