Hi,

Many thanks for pointers.

Actually everything worked fine when I tried to perform GO analysis for the
genes which are within 20 KB upstream and 10 KB downstream of a given
chromosomal region (CNV in my case) except GO analysis resulted in null. I
used following scripts:

source("http://bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")
biocLite("GenomicRanges")
library("ChIPpeakAnno")
library('GenomicRanges')
library(org.Hs.eg.db)
data=read.csv('C:/test.csv', header=T, sep=',')
myCNVdata=RangedData(IRanges(start=data$Start, end=data$End),
space=(data$Chr))
data(TSS.human.GRCh37)
annotatedPeak = annotatePeakInBatch (myCNVdata, AnnotationData =
TSS.human.GRCh37, output='both', maxgap=20000, select='all')
final_result=annotatedPeak[!c(annotatedPeak$insideFeature == 'upstream' &
annotatedPeak$shortestDistance>10000),]
enrichedGO <- getEnrichedGO (final_result, orgAnn="org.Hs.eg.db",
maxP=0.05, multiAdj =TRUE, minGOterm=1,  multiAdjMethod="BH")

But the enrichedGO has nothing except the column headings. When I tried do
do for first 5 rows(final_result[1:5,]), it works but when I do for all the
rows in "final_result" (333), it does not yield anything. I do not get any
error messages either.

Any idea on where am I doing wrong?

--Yadav



On Thu, May 17, 2012 at 5:05 PM, Zhu, Lihua (Julie)
<Julie.Zhu@umassmed.edu>wrote:

> Yadav,
>
> Please set parameters output = "both", maxgap = 100000, select="all"
> followed by filtering the results further using a combination of
> insideFeature and shortestDistance. For detailed parameter setting, please
> type help(annotatePeakInBatch) in a R session.
>
> For example, the following will return peaks located within 5kb downstream
> of a gene.
>
>  annotatedPeak[!is.na(annotatedPeak$insideFeature) &
> annotatedPeak$insideFeature == "downstream" &
> !is.na(annotatedPeak$shortestDistance) & annotatedPeak$shortestDistance
> <=5000,]
>
> Best regards,
>
> Julie
>
>
> On 5/17/12 4:17 PM, "Yadav Sapkota" <ysapkota@ualberta.ca> wrote:
>
> > Hi,
> >
> > I tried this function and it works fine for me however, I could not find
> any
> > option to define the upstream and downstream size while looking for
> > neighboring genes.
> >
> > For example, I wanted to only query genes that are located 100 KB
> upstream and
> > 50 KB downstream from a chromosomal range. Any hint would be appreciated.
> > Below is the code I am using for demo:
> >
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("ChIPpeakAnno")
> > library("ChIPpeakAnno")
> > data(myPeakList)
> > data(TSS.human.GRCh37)
> > annotatedPeak = annotatePeakInBatch (myPeakList[1:6,], AnnotationData =
> > TSS.human.GRCh37)
> >
> > --Yadav
> >
> >
> >
> >
> > On Thu, May 17, 2012 at 10:52 AM, Zhu, Lihua (Julie) <
> Julie.Zhu@umassmed.edu>
> > wrote:
> >> Yadav,
> >>
> >> You could try annotatePeakInBatch in ChIPpeakAnno package.
> >>
> >> Best regards,
> >>
> >> Julie
> >>
> >>
> >> On 5/17/12 12:40 PM, "Yadav Sapkota" <ysapkota@ualberta.ca> wrote:
> >>
> >>> Hi,
> >>>
> >>> Is there any tool or package that can query neighboring genes (lets
> say 100
> >>> KB upstream and downstream) of a specific chromosomal range
> (chr1:100-200)?
> >>> I have thousands of these chromosomal ranges.
> >>>
> >>> You help will be greatly appreciated.
> >>>
> >>> Regards,
> >>> Yadav Sapkota
> >>> Uni of Alberta
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >
> >
>
>
>


-- 
Yadav Sapkota
PhD Candidate
Dept. of Laboratory Medicine and Pathology, UofA
Cross Cancer Institute
11560 University Avenue, Edmonton AB T6G 1Z2
Phone: 780-5778092

	[[alternative HTML version deleted]]

