configuration-class: Class '"configuration"'

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

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 <[e-mail]>

See Also

SeqObj cobindr

Examples

showClass("configuration")

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