Hi, I want to check peak overlap between two chip-seq datasets using ChiPpeakAnno package. When I try to read the MACS output file with the code provided in the vignette it shows the following error.

brg1bed <- system.file("extdata", "brg1.bed", package="ChIPpeakAnno")

grbrg1 <- toGRanges(brg1bed, format="BED", header=FALSE)

Error in read.table(data, header = header, comment.char = comment.char, :

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

I have replaced the "extdata" to my working directory but it still showed error.

When I read MACS output with read.delim it showed the same error

sl1bed <- system.file("chip brg1", "sl1.txt", package="ChIPpeakAnno")

grsl1 <- toGRanges(sl1bed, format="MACS", header=FALSE)

Error in read.table(data, header = header, comment.char = comment.char, :

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.

Any suggestion would be appreciated.

suppose your brg1.bed is in current working directory, please try to run:

grbrg1 <- toGRanges("brg1.bed", format="BED", header=FALSE)

Thank you for your response, Jianhong. I tried what you suggested and got this error, even thought my working directory does contain brg1.bed file

brg1bed <- system.file("extdata", "brg1.bed", package="ChIPpeakAnno")

grbrg1 <- toGRanges("brg1bed", format="BED", header=FALSE)

Error in file(file, "rt") : cannot open the connection

In addition: Warning message:

In file(file, "rt") : cannot open file 'brg1bed': No such file or directory.

Could you please tell me what is the "extdata" in the code? is it a directory within the package where I am importing the data?

Sure, I will go through it. Indeed it was a typo error as changing brg1bed to brg1.bed worked out. Thank you for your time.