How to upload my own data set to analyse in ChIPseeker
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@anasastreperona-9284
Last seen 5.9 years ago
United States

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 

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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.

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