YaqcControlProbes-class: Class "YaqcControlProbes"

In yaqcaffy: Affymetrix expression data quality control and reproducibility analysis

Description

The YAQCStats class stores the probes used for the quality control as a special class, namely the YaqcControlProbes class. This class encapsulated the probe names that are used the generate an YAQCStats object. Objects of this class are created with the probeSelectionInterface function. The hybridization, labelling and degradation probes are encapsulated in YaqcBioProbes, YaqcSpkProbes and YaqcDegProbes objects respectively. These can be retrieved with their respective accessors, as described below. Furthermore, an info function allows to retrieve or set a free text slot to describe the YaqcControlProbes object.

Slots

bio:

Object of class "YaqcBioProbes" encapsulating the 'bio' (BioB5, BioB3, BioBM, BioC5,...) hybridization probes.

spk:

Object of class "YaqcSpkProbes" encapsulating the labelling probes (dap5, dap3, dap3, phe5,...).

deg:

Object of class "YaqcDegProbes" encapsulating the degradation probes used to assess the 3'/5' ratio.

info:

Object of class "character" providing general information about the YaqcControlProbes object.

Methods

bio

signature(object = "YaqcControlProbes"): returns the 'bio' (BioB5, BioB3, BioBM, BioC5,...) hybridization probes of the current object, as an YaqcBioProbes instance.

bio

signature(object = "YaqcBioProbes"): returns the 'bio' (BioB5, BioB3, BioBM, BioC5,...) hybridization probes of the current object, as characters.

spk

signature(object = "YaqcControlProbes"): returns the labelling probes (dap5, dap3, dap3, phe5,...) of the current object, as an YaqcSpkProbes instance.

spk

signature(object = "YaqcSpkProbes"): returns the labelling probes (dap5, dap3, dap3, phe5,...) of the current object, as characters

deg

signature(object = "YaqcControlProbes"): returns the degradation probes used to assess the 3'/5'ratio, as an YaqcDegProbes instance.

deg

signature(object = "YaqcDegProbes"): returns the degradation probes used to assess the 3'/5'ratio, as characters.

info

signature(object = "YaqcControlProbes"): returns the inforation slot of the current object.

info<-

signature(object = "YaqcControlProbes"): sets the information slot of the current object.

show

signature(object = "YaqcControlProbes"): shows the current object.

Author(s)

Laurent Gatto

See Also

probeSelectionInterface and YAQCStats

Examples

showClass("YaqcControlProbes")
showClass("YaqcBioProbes")
showClass("YaqcSpkProbes")
showClass("YaqcDegProbes")

yaqcaffy documentation built on Nov. 8, 2020, 8:31 p.m.