Entering edit mode
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/i
nst/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
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