Yadav, Try this and see if you get anything. If you do, that means you need to set the filtering criteria maxP less stringent. enrichedGO <- getEnrichedGO (final_result, orgAnn="org.Hs.eg.db", maxP=1, multiAdj =TRUE, minGOterm=1, multiAdjMethod="BH") Best regards, Julie On 5/22/12 4:20 PM, "Yadav Sapkota" <ysapkota@ualberta.ca> wrote: 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$shortestDistance>10000),] enrichedGO <- getEnrichedGO (final_result, orgAnn="org.Hs.eg.db", maxP=0.05, multiAdj =TRUE, minGOterm=1, multiAdjMethod="BH") But the enrichedGO has nothing except the column headings. When I tried do do for first 5 rows(final_result[1:5,]), it works but when I do for all the rows in "final_result" (333), it does not yield anything. I do not get any error messages either. Any idea on where am I doing wrong? --Yadav On Thu, May 17, 2012 at 5:05 PM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: Yadav, Please set parameters output = "both", maxgap = 100000, select="all" followed by filtering the results further using a combination of insideFeature and shortestDistance. For detailed parameter setting, please type help(annotatePeakInBatch) in a R session. For example, the following will return peaks located within 5kb downstream of a gene. annotatedPeak[!is.na <http: is.na=""> (annotatedPeak$insideFeature) & annotatedPeak$insideFeature == "downstream" & !is.na <http: is.na=""> (annotatedPeak$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 >> >> > > [[alternative HTML version deleted]]