How to load fasta file with openPrimeR?
but if I give these commands to a local file:
```
fasta.file <- system.file("extdata", "IMGT_data", "templates",
"stx.fa", package = "openPrimeR")
fasta.file <- system.file("stx.fa", package = "openPrimeR")
```
where stx.fa il the file I wanted to open and that is present in the
working directly. I get only an empty object.
If "stx.fa" is in fact in the current working directory then use fasta.file <- "stx.fa" system.file() is for accessing files in installed packages. -Bill On Mon, Feb 15, 2021 at 10:11 AM Luigi Marongiu
<marongiu.luigi at gmail.com> wrote:
Hello, I am trying to load a fast file with the package 'openPrimeR'. The manual (https://www.bioconductor.org/packages/release/bioc/vignettes/openPrimeR/inst/doc/openPrimeR_vignette.html) says to use: ``` fasta.file <- system.file("extdata", "IMGT_data", "templates", "Homo_sapiens_IGH_functional_exon.fasta", package = "openPrimeR") # Load the template sequences from 'fasta.file' seq.df.simple <- read_templates(fasta.file) ``` but if I give these commands to a local file: ``` fasta.file <- system.file("extdata", "IMGT_data", "templates", "stx.fa", package = "openPrimeR") fasta.file <- system.file("stx.fa", package = "openPrimeR") ``` where stx.fa il the file I wanted to open and that is present in the working directly. I get only an empty object. What am I getting wrong? Thank you -- Best regards, Luigi
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