ChIPpeakAnno
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Gaurav, You could use the following code to read in your peak file where ~/dataset/peaks1.bed contains the peaks in bed format. Library(ChIPpeakAnno) peaks1= BED2RangedData(read.table("~/dataset/peaks1.bed", sep="\t")) For detailed information on how to use ChIPpeakAnno, please type vignette("ChIPpeakAnno") Also, you might want to read the paper http://www.biomedcentral.com/1471-2105/11/237 Best regards, Julie On 3/16/13 10:34 AM, "Gaurav Pandey" <gaurav.pandey789 at="" gmail.com=""> wrote: > Hello, > I wanted to use the package CHIPpeakAnno, for my project work > Can you please tell me how can I upload my own chip seq peak file and use > annotate using CHIPpeakAnno. > > Thank you. > Regards
annotate ChIPpeakAnno annotate ChIPpeakAnno • 784 views
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Gaurav, Did you try to download the package using the following code in a R session? To use all the functions, please install R 2.15.2. source("http://bioconductor.org/biocLite.R") biocLite("ChIPpeakAnno") If you still have problem, could you please send the sessionInfo()? Could you please also copy bioconductor@r-project.org? Thanks! Best regards, Julie On 3/17/13 1:58 PM, "Gaurav Pandey" <gaurav.pandey789@gmail.com> wrote: Thanks a lot Ma'am..but i am not able to install the package.., it gave folllowing errors: Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open the connection In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 4676560 != reported length 18821426 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'BSgenome.Ecoli.NCBI.20080805/DESCRIPTION', probable reason 'No such file or directory' Regards [[alternative HTML version deleted]]
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Gaurav, You could read the output file into R using the following code, assuming the output file has a header and is tab-delimited. X = read.table(“sissrsoutput.txt”, sep="\t", header=TRUE) Then convert X to RangedData using the following line of code assuming you have a named column start (start of the peak), end (end of the peak) and chromosome (chromosome of the peak). PeaksRD = RangedData(IRanges(start = X$start, end=X$end), space=X$chromosome) Best regards, Julie On 3/29/13 8:06 AM, "Gaurav Pandey" <gaurav.pandey789@gmail.com> wrote: Ma'am how to use it for Sissrs output (a tesxt file) ? Regards On Mon, Mar 18, 2013 at 6:45 PM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: Gaurav, Did you try to download the package using the following code in a R session? To use all the functions, please install R 2.15.2. source("http://bioconductor.org/biocLite.R <http: bioconductor.org="" bioclite.r=""> ") biocLite("ChIPpeakAnno") If you still have problem, could you please send the sessionInfo()? Could you please also copy bioconductor@r-project.org <http: bioconductor@r-project.org=""> ? Thanks! Best regards, Julie On 3/17/13 1:58 PM, "Gaurav Pandey" <gaurav.pandey789@gmail.com <http:="" gaurav.pandey789@gmail.com=""> > wrote: Thanks a lot Ma'am..but i am not able to install the package.., it gave folllowing errors: Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open the connection In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 4676560 != reported length 18821426 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'BSgenome.Ecoli.NCBI.20080805/DESCRIPTION', probable reason 'No such file or directory' Regards [[alternative HTML version deleted]]
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