[Bioc-sig-seq] passing sequences on the fly to cosmo()

[Ivan Gregoretti]

Hello everybody,

The package cosmo is used for detection of motifs.

In it's simplest form, you can run it successfully with only three commands:

library(cosmo)
seqFile <- system.file("Exfiles/seq.fasta", package = "cosmo")
results <- cosmo(seqs = seqFile, minW = 7, maxW = 8, models = c("OOPS", "TCM"))


Note:
In this case, seqs takes a connection to a fasta file.


My question:
Can anybody give me a hand to figure out how to pass sequences to seqs
without using a file?


The documentation (?cosmo) says:
seqs: This argument specifies the sequences to be analyzed.  If seqs
== "browse", a browser appears that allows the user to select a file
that contains the sequences in FASTA format. If seqs is another
character string, it is assumed to give the path to a FASTA file
containing the sequences of interest.  Lastly, seqs may be a list with
each element representing a sequence in the form of a single string
such as "ACGTAGCTAG" ("seq" entry) and a description ("desc" entry).


The package's author:
I contacted him but he does not work in this anymore. Dead end.


Thank you,

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878