| write.sequences {cobindR} | R Documentation |
writes the sequences of a cobindr-object into a fasta file.
## S4 method for signature 'cobindr' write.sequences(x, slotname = "sequences", file = NULL)
x |
an object of the class "cobindr", which will hold all necessary information about the sequences. |
slotname |
string, describing whether to use foreground sequences (default) or background sequences |
file |
path to file. If filename is 'NULL' a filename is generated based on the name of the object of class "cobindr". |
Stefan Kroeger <kroeger@informatik.hu-berlin.de>
write.bindingsites.table, write.bindingsites, write.pairs, write
cfg <- cobindRConfiguration()
sequence_type(cfg) <- 'fasta'
sequence_source(cfg) <- system.file('extdata/example.fasta', package='cobindR')
# avoid complaint of validation mechanism
pfm_path(cfg) <- system.file('extdata/pfms',package='cobindR')
pairs(cfg) <- ''
runObj <- cobindr(cfg)
write.sequences(runObj, file = file.path(tempfile("example.txt",tempdir())) )