Clarrification of ReadDNAStringSet
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@khouloudmadbouh-7264
Last seen 7.7 years ago
France

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?

 

sequencing • 1.8k views
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@steve-lianoglou-2771
Last seen 26 days ago
United States

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)

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Maybe filepath1 = file.choose() will help; on some platforms it pops up the familiar file navigation dialog box.

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@khouloudmadbouh-7264
Last seen 7.7 years ago
France

Ok thank you 

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