Oleg,

Thanks for the detailed information!  I tried and it works.

You need input nearestStart as output parameter instead of nearest_start. By default it will calculate nearestStart. I will add better error message later.

data(myPeakList)
data(TSS.human.NCBI36)
annotatedPeak = annotatePeakInBatch(myPeakList[1:6, ], AnnotationData = TSS.human.NCBI36,output='nearestStart', PeakLocForDistance='middle', FeatureLocForDistance='TSS')

 ?annotatePeakInBatch will give you more information about other parameters.

Please let me know if you still have problems.

Best regards,

Julie

On 10/21/10 10:59 AM, "Oleg Mayba" <oleg.mayba@gmail.com> wrote:

Hi, Julie
I encountered this problem with R 2.12.0.
I just tried this with R 2.11.1 and I  can't replicate the exact call  because the version of ChIPpeakAnno for that R version doesn't have arguments Peak LocForDistance and FeatureLocForDistance, but it still gives me same error even if I don't specify these arguments (see below).
Thanks!
Oleg.

> library('ChIPpeakAnno')
> data(myPeakList)
> ensembl=useMart('ensembl', dataset='hsapiens_gene_ensembl')
Checking attributes ... ok
Checking filters ... ok
> TSS=getAnnotation(ensembl, featureType='TSS')
> annotated_peaks=annotatePeakInBatch(myPeakList, AnnotationData=TSS, output='nearest_start', PeakLocForDistance='middle', FeatureLocForDistance='TSS')
Error in annotatePeakInBatch(myPeakList, AnnotationData = TSS, output = "nearest_start",  :
  unused argument(s) (PeakLocForDistance = "middle", FeatureLocForDistance = "TSS")
> annotated_peaks=annotatePeakInBatch(myPeakList, AnnotationData=TSS, output='nearest_start')
Error in annotatePeakInBatch(myPeakList, AnnotationData = TSS, output = "nearest_start") :
  object 'r.output' not found
> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

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

other attached packages:
 [1] ChIPpeakAnno_1.4.2                  limma_3.4.5                         org.Hs.eg.db_2.4.1
 [4] GO.db_2.4.1                         RSQLite_0.9-2                       DBI_0.2-5
 [7] AnnotationDbi_1.10.2                BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.16.5
[10] GenomicRanges_1.0.9                 Biostrings_2.16.9                   IRanges_1.6.17
[13] multtest_2.5.14                     Biobase_2.8.0                       biomaRt_2.4.0

loaded via a namespace (and not attached):
[1] MASS_7.3-6      RCurl_1.4-4.1   splines_2.11.1  survival_2.35-8 tools_2.11.1    XML_3.2-0.1
>

On Thu, Oct 21, 2010 at 5:51 AM, Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu> wrote:
Oleg,

I will look into this. Did you encounter this problem in R 2.11? Thanks!

Best regards,

Julie



On 10/20/10 10:46 PM, "Oleg Mayba" <oleg.mayba@gmail.com <http://oleg.mayba@gmail.com> > wrote:

Hi, Julie
Thanks for putting this package out there. I seem to have encountered a bug or at least an uninformative error message (please see below) and I would appreciate a clarification.
Thanks!
 Oleg.


troublesome code snippet:


library('ChIPpeakAnno')
data(myPeakList)
ensembl=useMart('ensembl', dataset='hsapiens_gene_ensembl')
TSS=getAnnotation(ensembl, featureType='TSS')
annotated_peaks=annotatePeakInBatch(myPeakList, AnnotationData=TSS, output='nearest_start', PeakLocForDistance='middle', FeatureLocForDistance='TSS')


This results in:

Error in annotatePeakInBatch(myPeakList, AnnotationData = TSS, output = "nearest_start",  :
  object 'r.output' not found


Here's session info:

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] ChIPpeakAnno_1.5.5                  limma_3.5.21
 [3] org.Hs.eg.db_2.4.6                  GO.db_2.4.5
 [5] RSQLite_0.9-2                       DBI_0.2-5
 [7] AnnotationDbi_1.11.9                BSgenome.Ecoli.NCBI.20080805_1.3.16
 [9] BSgenome_1.17.7                     GenomicRanges_1.1.38
[11] Biostrings_2.17.48                  IRanges_1.7.39
[13] multtest_2.5.14                     Biobase_2.9.2
[15] biomaRt_2.5.1

loaded via a namespace (and not attached):
[1] MASS_7.3-8      RCurl_1.4-3     splines_2.12.0  survival_2.35-8
[5] tools_2.12.0    XML_3.2-0
>














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