cobindr-class: Class '"cobindr"'
In cobindR: Finding Co-occuring motifs of transcription factor binding sites

Description Objects from the Class Slots Methods Author(s) See Also Examples

Container for experiment run and its meta-data

Objects can be created by calls of the form new("cobindr", conf, name, desc).

uid:: Object of class "character" ~~ unique id for internal representation
name:: Object of class "character" ~~ name of the experiment
sequences:: Object of class "list" ~~ list of sequence objects to be analyzed
bg_sequences:: Object of class "list" ~~list of background sequences for statistical analyses
desc:: Object of class "character" ~~ verbal experiment description
configuration:: Object of class "configuration" ~~the configuration object used to describe the experiment
pfm:: Object of class "list" ~~list of pfms to be used
binding_sites:: Object of class "data.frame" ~~ data frame for predicted binding sites. Data frame structure: uid:integer, seqObj_uid:integer, pfm:factor, start:integer, end:integer, score:double, seq:character, strand:factor, source:factor.
bg_binding_sites:: Object of class "data.frame" ~~ data frame for predicted binding sites in the background sequences. Data frame structure: uid:integer, seqObj_uid:integer, pfm:factor, start:integer, end:integer, score:double, seq:character, strand:factor, source:factor.
pairs:: Object of class "data.frame" ~~ data frame for predicted pairs of transcription factors. Data frame structure: uid:integer, seqObj_uid:integer, pair:factor, bs_uid1:integer, bs_uid2:integer, distance_start:integer.
bg_pairs:: Object of class "data.frame" ~~ data frame for predicted pairs of transcription factors in the background sequences. Data frame structure: uid:integer, seqObj_uid:integer, pair:factor, bs_uid1:integer, bs_uid2:integer, distance_start:integer.
pairs_of_interest:: Object of class "factor" ~~ contains pairs for search