cobindr-class {cobindR} | R Documentation

## Class `"cobindr"`

### Description

Container for experiment run and its meta-data

### Objects from the Class

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

### Slots

`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

### Methods

detrending

  `signature(object = "cobindr")`: ...

find.pairs

  `signature(object = "cobindr")`: ...

generate.background

  `signature(object = "cobindr")`: ...

get.bindingsite.ranges

  `signature(object = "cobindr")`: ...

get.pairs

  `signature(object = "cobindr")`: ...

get.significant.pairs

  `signature(object = "cobindr")`: ...

initialize

  `signature(.Object = "cobindr")`: ...

input.pwm

  `signature(object = "cobindr")`: ...

plot.detrending

  `signature(object = "cobindr")`: ...

plot.gc

  `signature(object = "cobindr")`: ...

plot.pairdistance

  `signature(object = "cobindr")`: ...

plot.pairdistribution

  `signature(object = "cobindr")`: ...

plot.positionprofile

  `signature(object = "cobindr")`: ...

plot.positions.simple

  `signature(object = "cobindr")`: ...

plot.positions

  `signature(object = "cobindr")`: ...

plot.tfbs.heatmap

  `signature(object = "cobindr")`: ...

plot.tfbs.venndiagram

  `signature(object = "cobindr")`: ...

plot.tfbslogo

  `signature(object = "cobindr")`: ...

predicted2pwm

  `signature(object = "cobindr")`: ...

rtfbs

  `signature(object = "cobindr")`: ...

search.gadem

  `signature(object = "cobindr")`: ...

search.pwm

  `signature(object = "cobindr")`: ...

testCpG

  `signature(object = "cobindr")`: ...

write.bindingsites.table

  `signature(object = "cobindr")`: ...

write.bindingsites

  `signature(object = "cobindr")`: ...

write.sequences

  `signature(object = "cobindr")`: ...

write

  `signature(x = "cobindr", file = "character")`: ...

### Author(s)

Manuela Benary <manuela.benary@cms.hu-berlin.de>

### See Also

`SeqObj` `configuration`

### Examples

    showClass("cobindr")

[Package cobindR version 1.24.0 Index]