Muhammad,

Please keep the email in the list for information sharing.

The myPeakList in the example is a build-in test dataset. You will need to use read.table to read your data in R. Conversion functions BED2RangedData and GFF2RangedData can be used for converting BED and GFF formatted dataset to RangedData before calling annotatePeakInBatch. To construct RangedData from other formats, please see help(RangedData) in IRanges package ( http://www.bioconductor.org/packages/2.7/bioc/html/IRanges.html).

For details, please refer the menu and paper at
http://www.bioconductor.org/packages/2.7/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf
http://www.biomedcentral.com/1471-2105/11/237

Please make sure you search the Bioc mailing archive since others might have posted similar questions.

Best regards,

Julie

On 1/6/11 1:39 AM, "muhammed shafi" <safee86@gmail.com> wrote:



On Tue, Dec 28, 2010 at 8:28 PM, Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu> wrote:
Muhammad,

Please update your R and Bioconductor installation to the most recent release (Bioconductor 2.7  and R 2.12.0) that should resolve the issue.

Best regards,

Julie



On 12/28/10 12:20 AM, "muhammed shafi" <safee86@gmail.com <http://safee86@gmail.com> > wrote:


Respected Madam,

I am new to bioinformatics and bioconductor
I am using R version 2.9.2 through linux(ubuntu) and bioconductor version2.4.
While I am trying to download ChIPpeakAnno package by giving following command

>source("http://www.bioconductor.org/biocLite.R" <http://www.bioconductor.org/biocLite.R%22> )
>biocLite("ChIPpeakAnno")

its giving an error saying


""Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  argument 'lib' is missing: using '/home/mlscubl11/R/i486-pc-linux-gnu-library/2.9'
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘ChIPpeakAnno’ is not available""


. Please help me to find out the problem. i am really sorry for mistakes in language.



thanking you

Muhammad shafi


hello,
thanks. i successfully installed this package.
i need to know about myPeakList. is it our data of interest or the data available in the package?

if it is our data of interest, how wil i read the data?
my data look like following
































ProbeName ChrCoordinates
A_17_P09533566 chr14:105445257-105445302
A_17_P17446523 chrY:9193800-9193844
A_17_P00145611 chr1:38478026-38478085
A_17_P00523928 chr1:155246905-155246951














































in an excel file. i want to know the nearest TSS for this coordinaes.how will i do that?
really sorry for my mistakes.


regards
muhammad







	[[alternative HTML version deleted]]

