I'm posting this error here to have a clearer idea of what's going on. 

I'm running tximport using my own dataset and following and modifying the instructions on the vignette. But I have found an issue and I can't get around it.

I have specified my working directory under the variable dir as follows:

dir <- '/Users/ctl/data/samples/experiment/salmon'

and I have created my files as follows:

files <- file.path(dir, samples$run, "quant.genes.sf")

which gives me an output like this:

"/Users/ctl/data/samples/experiment/salmon/run_1/quant.genes.sf"

Now, if I add the sample name as follows:

names(files) <- paste0(samples$run)

I get this:

                                                                                               run_1

"/Users/ctl/data/samples/experiment/salmon/run_1/quant.genes.sf"

                                                                                               run_2

"/Users/ctl/data/samples/experiment/salmon/run_2/quant.genes.sf"

And this result agrees with what I have in that directory and inside each sample folder. However, when I check if all files are listed, I get this error:

all(file.exists(files))

FALSE

In my previous (misplaced) post on GitHub issues, I was told that I am not providing the right directory for the files, but it seem I am providing it correctly. Any hints to how can I solve this problem?

Thanks in advance!

You can try:

file.exists(files)

To see if all or just some are not present at the location you specified. 

If they are all not present, make sure you have specified the path correctly. You can work backwards, e.g.:

file.exists("/Users/ctl/data/samples/experiment/salmon")

file.exists("/Users/ctl/data/samples/experiment")

...

Hi!

Yes, that helped me to solve the problem. There was an issue with my sample file. 

Thanks a lot for the support.