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hartleys / JunctionSeq

The JunctionSeq R package is a powerful tool for testing and visualizing differential usage of exons and splice junctions in next-generation, high-throughput RNA-Seq experiments.
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error in reading decoder file #46

Open CS791 opened 4 years ago

CS791 commented 4 years ago

Hi! I am using JunctionSeq first time and not very expert in R language. While running JunctionSeq analysis I am getting an error in reading decoder file. Here is the command and error: "#Read the decoder: decoder.file <- system.file("~/R/Splicejunction/annoFiles/decoder.bySample.txt", package="JunctionSeq"); decoder <- read.table(decoder.file, header=TRUE, stringsAsFactors=FALSE)"

"Error in read.table(decoder.file, header = 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"

Any help is much appreciated.

Thanks CS

hartleys commented 4 years ago

the system.file invocation from the vignette is just to get the special files that come with the vignette. Replace the whole thing with the file name. Also to be safe I would use the full path instead of the tilde. So like:

decoder.file <- "/home/blahblah/R/Splicejunction/annoFiles/decoder.bySample.txt"

Then run the rest as is