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  • Bioconductor package -GADEM

    Hello Everyone
    I am new to R, and I am trying to use the bioconductor package rGADEM to do de nova motif analysis -
    I would like to know what these commands do -

    > pwd <- ""
    > path <- system.file("extdata/Test_100.fasta", package = "rGADEM")
    > FastaFile <- paste(pwd, path, sep = "")
    > Sequences <- read.DNAStringSet(FastaFile, "fasta")


    I am getting error messages when I run the last command , understanding the commands would help me overcome the frustration.

    The error message I got was
    (Call2("new_input_ExternalFilePtr", fp, PACKAGE = "Biostrings") :
    cannot open file ''
    In addition: Warning message:
    'read.DNAStringSet' is deprecated.
    Use 'readDNAStringSet' instead.
    See help("Deprecated")


    Thanks

  • #2
    error message means you have to install the Biostrings package, which contains several functions including the one missing "readDNAStringSet" (and it's telling you that "read.DNAStringSet" is no longer used).

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