Hi Khademul,

Thanks for your interest!

The package is developed for R 2.10.0. The dataset myPeakList and
TSS.human.NCBI36 were RangedData object. The implementation of RangedData
class in R 2.10.0 is not back compatible with the RangedData in R 2.9.0.

The peaks need to be in RangedData format for the function
annotatePeakInBatch to work.

Here is how to create a RangedData from a peak list where start is the start
of the binding site, end is the end of the binding site, names is the name
of the binding site, space is the chromosome name where the binding site is
located.
If you think having a conversion function bed2RangedData is useful, I will
add it to the next release.
myexp = RangedData(IRanges(start = c(967654, 2010897, 2496704,

 3075869, 3123260, 3857501, 201089), end = c(967754, 2010997,

 2496804, 3075969, 3123360, 3857601, 201089), names = c("Site1",

 "Site2", "Site3", "Site4", "Site5", "Site6", "site7")), space = c("1",

 "2", "3", "4", "5", "6", "2"))

Please let me know if it works for you in R 2.10.0.

Best regards,

Julie

*******************************************
Julie Zhu, Ph.D
Research Associate Professor
Program Gene Function and Expression
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256



On 11/27/09 11:11 AM, "Khademul Islam" <khademul.islam@gmail.com> wrote:

> Hi,
> 
> It seems that this is a very interesting package.
> I am very interested to use this package. I installed the package and load the
> library and dependencies without any problem. I try to follow exactly your
> given example at first........................ but it gave following error at
> the beginning
> 
> library(ChIPpeakAnno)
> data(myPeakList)
> data(TSS.human.NCBI36)
> annotatedPeak = annotatePeakInBatch(myPeakList[1:6,],
> AnnotationData=TSS.human.NCBI36)
> as.data.frame(annotatedPeak)
> 
> 
>> >
>> >
>> > library(ChIPpeakAnno)
>> > data(myPeakList)
> 
>> > data(TSS.human.NCBI36)
>> > annotatedPeak = annotatePeakInBatch(myPeakList[1:6,],
>> AnnotationData=TSS.human.NCBI36)
> 
> Error in seq_len(ncol(x)) : argument must be non-negative
>> > as.data.frame(annotatedPeak)
> Error: object 'annotatedPeak' not found
> Error in as.data.frame(annotatedPeak) :
>   error in evaluating the argument 'x' in selecting a method for function
> 'as.data.frame'
> 
> 
> 
> 
> following is the session Info:
> 
> 
>> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;L
> C_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS
> =C;LC_TELEPHONE=C;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_1.2.0                  org.Hs.eg.db_2.2.11
>  [3] GO.db_2.2.11                        RSQLite_0.7-1
> 
>  [5] DBI_0.2-4                           AnnotationDbi_1.6.0
>  [7] BSgenome.Ecoli.NCBI.20080805_1.3.13 BSgenome_1.12.5
>  [9] Biostrings_2.12.10                  IRanges_1.2.3
> 
> [11] multtest_2.1.1                      Biobase_2.4.1
> [13] biomaRt_2.0.0
> 
> loaded via a namespace (and not attached):
> [1] MASS_7.2-47     RCurl_0.98-1    splines_2.9.0   survival_2.35-4
> 
> [5] tools_2.9.0     XML_2.5-1
>> > 
> 
> 
> 
> 
> 
> ### Could you please tell me how can I solve this ??
> 
> ## My second question is : in which format I have to provide my real peak
> file. (Bed, wig...etc ???) Which format this package it accepts? It would be
> helpful you provide a text file showing example of peakfile.
> 
> 
> Could you please help
> 
> 
> Thank you
> 
> Khademul
> 


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