Hi everybody,

I have just started using featuercounts and am new to this. Would you please help me with the folowing:

>fls <- dir("/path/to/bam/files/", "bam$")
> fls
 [1] "X_A.bam" 
> props <- propmapped(files=fls)
Error in normalizePath(files, mustWork = T) :
  path[1]="ENCFF064QSN.bam": No such file or directory

I can see that bam files are assigned but can't call them.

Thank you in advance, Memol

You haven't told propmapped which directory the files are in so, naturally enough, it can't find them.

You need something like

bamdir <- "/path/to/bam/files"
bamfiles <- dir(bamdir, pattern = "bam$")
props <- propmapped( file.path(bamdir,bamfiles) )

Note that in the very latest version of Rsubread, you don't need to run propmapped at all, because the proportion of reads mapped is already returned as a data.frame from align() or subjunc().