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Old 10-15-2012, 09:55 AM   #1
DNASpeaks
Junior Member
 
Location: USA

Join Date: Oct 2012
Posts: 5
Default 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
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Old 06-04-2013, 06:52 AM   #2
araposo
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Location: Lisbon, Portugal

Join Date: Aug 2012
Posts: 2
Default

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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