configuration-class {cobindR} | R Documentation

## Class `"configuration"`

### Description

Container for experiment description.

### Objects from the Class

Objects can be created by calls of the form `new("configuration", fname)`.

### Slots

`id`:

  Object of class `"character"` ~~ unique id for internal representation

`experiment_description`:

  Object of class `"character"` ~~ verbal experiment description

`sequence_source`:

  Object of class `"character"` ~~ file path or list of paths

`sequence_origin`:

  Object of class `"character"` ~~ source of sequence data, e.g. ensembl

`sequence_type`:

  Object of class `"character"` ~~ either ChipSeq or Fasta or BED are available

`bg_sequence_source`:

  Object of class `"character"` ~~ file path or list of paths

`bg_sequence_origin`:

  Object of class `"character"` ~~ how the background is obtained - either simulated or from fasta files or from gene ids

`bg_sequence_type`:

  Object of class `"character"` ~~ determines the generation of the background sequences. Possible values: simulated, fasta and geneid

`species`:

  Object of class `"character"` ~~ reference species

`downstream`:

  Object of class `"numeric"` ~~ length of sequence downstream of reference point, e.g. transcription start site

`upstream`:

  Object of class `"numeric"` ~~ length of sequence upstream of reference point, e.g. transcription start site

`max_distance`:

  Object of class `"numeric"` ~~ maximal distance allowed between cooccuring transcription factor binding sites

`pairs`:

  Object of class `"character"` ~~ list of pairs of interesting transcription factors

`pfm_path`:

  Object of class `"character"` ~~ path to pfm matrix file

`threshold`:

  Object of class `"numeric"` ~~ threshold for transcription factor binding site prediction

`fdrThreshold`:

  Object of class `"numeric"` ~~ false discovery rate for filtering results (used in rtfbs)

`date`:

  Object of class `"character"` ~~ data of experiment run

`path`:

  Object of class `"character"` ~~ path of configuration file

`mart`:

  Object of class `"character"` ~~ optional mirror for biomart

`pseudocount`:

  Object of class `"numeric"` ~~ sets the pseudocount for the detrending analysis

`pValue`:

  Object of class `"numeric"` ~~ optional p-Value for search with RGadem

### Methods

initialize

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

read.background.fasta

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

read.pfm

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

read.sequences

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

write

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

### Author(s)

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

### See Also

`SeqObj` `cobindr`

### Examples

    showClass("configuration")

[Package cobindR version 1.24.0 Index]