I think the problem is system.file, which is R base, but I'll go for bioconductor. Thanks
On Mon, Feb 15, 2021 at 7:18 PM Bert Gunter <bgunter.4...@gmail.com> wrote: > > As this is a Bioconductor package, why not ask on their support page: > > https://support.bioconductor.org/ > > > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Mon, Feb 15, 2021 at 10:11 AM Luigi Marongiu <marongiu.lu...@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 >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. -- Best regards, Luigi ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
