write.sequences: writes the sequences of a cobindr-object into a fasta file.

In cobindR: Finding Co-occuring motifs of transcription factor binding sites

Description

writes the sequences of a cobindr-object into a fasta file.

Usage

## S4 method for signature 'cobindr'
write.sequences(x, slotname = "sequences", file = NULL)

Arguments

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".

Author(s)

Stefan Kroeger <[e-mail]>

See Also

write.bindingsites.table, write.bindingsites, write.pairs, write

Examples

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())) )

cobindR documentation built on April 28, 2020, 6:40 p.m.