Hello,

I am new to R and analyzing ChIPseq data.  I mapped my ChIP-seq reads by bowtie2 and called the peaks with MACS2 and got some output files, peaks.narrowPeak, peaks.xls, summits.bed. I am trying to use ChIPpeakAnno to do the downstream analysis, I used the following commands to convert MACS2 data to GRange :

> bed <- system.file("extdata", "605kct_F5FMX_peaks.narrowPeak", package="ChIPpeakAnno")

> gr1 <- toGRanges(bed, format="narrowPeak", header = FALSE)

Then I got the error message below:

Error in read.table(data, header = FALSE, fill = TRUE, stringsAsFactors = FALSE) :

  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.

Could someone let me know what is wrong with it?

Thank you for your help.

John 

I think you need to change peakfile path like:

bed <- "file/path/to/your/narrowPeak"

Hi Jianhong,

Thank you for the help. 

I added the path for the file in the first command line, but still get the same error.

> bed <- system.file("extdata", "C:/Users/name/Desktop/605chip/q0.001/605kct_F5FMX_peaks.narrowPeak", package="ChIPpeakAnno")
> gr1 <- toGRanges(bed, format="narrowPeak", header = FALSE)
Error in read.table(data, header = FALSE, fill = TRUE, stringsAsFactors = FALSE) : 
  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

John

Hi Julie,

Thank you for the suggestion.

With

bed <- "C:/Users/name/Desktop/605chip/q0.001/605kct_F5FMX_peaks.narrowPeak"

The narrowPeak file can be loaded, however, there are still some errors showed up:

John