Question: How to upload my own data set to analyse in ChIPseeker
0
gravatar for Ana.SastrePerona
3.9 years ago by
United States
Ana.SastrePerona0 wrote:

Hi every one, first at all sorry about my simple questions, but I'm beginner using R and also analysing ChIP seq data.

I've following the example to do the ChIP profiling and annotations using ChIPseeker, and everything was fine. But know I'm trying to do the analysis of my samples, and i'm not exactly sure how should I upload my dataset. I'm using readPeakFile for it.

> peakfile <- system.file("extdata", "peaks_fix30.bed", package = "ChIPseeker")
> peak.gr <- readPeakFile(peakfile, as = "GRanges")
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input
In addition: Warning message:
In file(file, "rt") :
  file("") only supports open = "w+" and open = "w+b": using the former

Can someone help me with this?

Thanks in advance,

Ana 

upload • 665 views
ADD COMMENTlink modified 3.9 years ago by Martin Morgan ♦♦ 23k • written 3.9 years ago by Ana.SastrePerona0

Hi Ana,

Please tag your question carefully e.g. you need to at least tag it with the name of the package you are using (ChIPseeker) so the author/maintainer of the package will get notified. Otherwise he'll probably never see your question.

Thanks,

H.

ADD REPLYlink written 3.9 years ago by Hervé Pagès ♦♦ 14k
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