Correct.

Julie


On 3/10/11 9:18 AM, "Jia Jin Kee" <jiajin@umich.edu> wrote:

Hi Julie,

To install the most recent version of chIPpeakAnno, should I update my R version first and then do

source("http://www.bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")


> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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                  GO.db_2.4.1
 [5] RSQLite_0.9-3                       DBI_0.2-5                           AnnotationDbi_1.10.2                BSgenome.Ecoli.NCBI.20080805_1.3.16
 [9] BSgenome_1.16.5                     GenomicRanges_1.0.9                 Biostrings_2.16.9                   IRanges_1.6.17
[13] multtest_2.6.0                      Biobase_2.8.0                       biomaRt_2.4.0

loaded via a namespace (and not attached):
[1] MASS_7.3-6      RCurl_1.4-2     splines_2.11.1  survival_2.35-8 tools_2.11.1    XML_3.2-0

On Thu, Mar 10, 2011 at 8:59 AM, Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu> wrote:
Jia,

I suspect that you have an old version of ChIPpeakAnno. Could you please install the most recent version and try again. Please let me know if you still encounters problem.

I just tried the example and it works.

Best regards,

Julie

 myexp =  RangedData(IRanges(start=c(1543200,1557200,1563000,1569800,167889600,100,1000),end=c(1555199,1560599,1565199,1573799,167893599,200,1200),names=c("p1","p2","p3","p4","p5","p6", "p7")),strand=as.integer(1),space=c(6,6,6,6,5,4,4))

   annotatedPeak= annotatePeakInBatch(myexp, AnnotationData = literature,PeakLocForDistance = "middle")

 sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] ChIPpeakAnno_1.6.0                  limma_3.6.9
 [3] org.Hs.eg.db_2.4.6                  GO.db_2.4.5
 [5] RSQLite_0.9-4                       DBI_0.2-5
 [7] AnnotationDbi_1.12.0                BSgenome.Ecoli.NCBI.20080805_1.3.16
 [9] BSgenome_1.18.2                     GenomicRanges_1.2.2
[11] Biostrings_2.18.2                   IRanges_1.8.8
[13] multtest_2.6.0                      Biobase_2.10.0
[15] biomaRt_2.6.0

loaded via a namespace (and not attached):
[1] MASS_7.3-9      RCurl_1.4-3     splines_2.12.1  survival_2.36-2 tools_2.12.1
[6] XML_3.2-0

>


On 3/9/11 11:58 PM, "Jia Jin Kee" <jiajin@umich.edu <http://jiajin@umich.edu> > wrote:

Hi Julie,

I realized that the reference manual is updated today and that the annotatePeakInBatch function now has two more arguments: PeakLocForDistance and FeatureLocForDistance. However when I tried the following R code:

     annPeak <- annotatePeakInBatch(peakData, AnnotationData=geneData, output="nearestStart", PeakLocForDistance="middle")

I got the following error message:

     Error in annotatePeakInBatch(peakData, AnnotationData = geneData, output = "nearestStart",  :
     unused argument(s) (PeakLocForDistance = "middle")

And when I typed ?annotatePeakInBatch in R, I could not find PeakLocForDistance and FeatureLocForDistance in the documentation.

Am I missing something here?

Thanks in advance
Jia Jin Kee






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