write.pairs: function to write output of findPairs into file

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

Description

Function writes the results of findPairs() as a tab-separated file. The file consists of 6 columns, namely

• a unique id for each pair,

• the unique id of the sequence, where the pair was found,

• the names of the corresponding PFMs,

• the unique id for each PFM, and

• the distance window in which the pair occurs.

Usage

## S4 method for signature 'cobindr'
write.pairs(x, file = NULL, background = FALSE)

Arguments

x	an object of the class "cobindr", which holds all necessary information about the sequences and the predicted binding sites.
file	path to file. If filename is 'NULL' a filename is generated based on the name of the object of class "cobindr".
background	logical flag. If background is 'TRUE' the pairs found in the background sequences are used.

Author(s)

Stefan Kroeger <[e-mail]>

See Also

write.bindingsites.table, write.bindingsites, write.sequences, write

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