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 > [[alternative HTML version deleted]]