Can't load files using system.file or file.path in R?

Question

I am using a program that requires me to load a "sam" file. However, the code given does not create the data.file variable necessary and instead produces "", a blank instead.

This is the code given:

data.file <- system.file(file.path('extdata', 'vignette-sam.txt'), package='flipflop')

I put in:

data.file <- system.file(file.path("Users", "User1", "Desktop", "Cond_18", 
                                   "Sorted_bam_files", "Cond_18_1.bam_sorted.sam"), 
                         package='flipflop')

The path is definitely correct and the package name is flipflop. However every time I check what the variable data.file is, it produces "". So the file is never being loaded and the script can't run.

I also put in the entire file path into one version of it:

data.file <- system.file('/Users/User1/Desktop/Cond_18/Sorted_bam_files/DBM_18_1.bam_sorted.sam', 
                         package='flipflop')

That version does not include file.path, but it is one of the script examples.

The line in the code that uses these variables is this:

if(preprocess.instance==''){
  print('PRE-PROCESSING sam file ....')
  data.file <- path.expand(path=data.file) # In case there is a '~' in the input path
  if(data.file==''){ print('Did you forget to give a SAM file?') ; return(NULL) } 
  annot.file   <- path.expand(path=annot.file)
  samples.file <- path.expand(path=samples.file)

And since data.file is "" it defaults to NULL.

Answer 1

You use system.file when the file you want to reference is from a package. Here is what the help file for system.file says:

Finds the full file names of files in packages etc.

You just want to reference a file on your machine. You can just directly store the path and use that as your data.file

data.file <- "C:/path/to/your/file"

The script uses file.path because it's a safer way to generate paths in a platform-independent way. For example:

> file.path("C:", "Users", "BotsRule", "Code", "myawesomeRscript.R")
[1] "C:/Users/BotsRule/Code/myawesomeRscript.R"

So the solution to your problem is to just make sure you're actually doing something just anything to correctly specify the path to your file.