Hi,

I have to use the ReadDNAStringSet function in order to extract sequences from Fasta file so i used this instruction:

filepath1 <- system.file("extdata", allgenes, package="Biostrings")

sequences <- readDNAStringSet(filepath1)

the readDNAStringSet function will extract sequences only if the input file is in the directory  "extdata" of the package Biostrings? how can I resolve this problem Please?

No, the function will read the file anywhere on the filesystem.

Packages usually include example (small sized) data in their extdata folders to show you how certain functions are run, which is why the examples use system.call('extdata', ..., package='Biostrings') to find it.

You just have to set filepath argument to be the path where your own data is (and, just to reiterate, do not put your data in the package's  extdata folder to read it)

Ok thank you