genomicProfilesInternal-class: Class '"genomicProfilesInternal"'

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Class "genomicProfilesInternal"

Description

Non exported class. Represents the stripped down version of genomicProfiles.

Objects from the Class

Created Internally.

Slots

PWM:

Object of class "matrix" ~~

PFM:

Object of class "matrix" ~~

PFMFormat:

Object of class "character" ~~

BPFrequency:

Object of class "vector" ~~

minPWMScore:

Object of class "vector" ~~

maxPWMScore:

Object of class "vector" ~~

profiles:

Object of class "GRList" ~~

DNASequenceLength:

Object of class "vector" ~~

averageExpPWMScore:

Object of class "vector" ~~

ZeroBackground:

Object of class "vector" ~~

drop:

Object of class "vector" ~~

tags:

Object of class "character" ~~

Methods

.averageExpPWMScore<-

signature(object = "genomicProfilesInternal", value = "numeric"): ...

.DNASequenceLength<-

signature(object = "genomicProfilesInternal", value = "vector"): ...

.drop<-

signature(object = "genomicProfilesInternal", value = "vector"): ...

.generatePWM

signature(object = "genomicProfilesInternal"): ...

.maxPWMScore<-

signature(object = "genomicProfilesInternal", value = "vector"): ...

.minPWMScore<-

signature(object = "genomicProfilesInternal", value = "vector"): ...

.profiles<-

signature(object = "genomicProfilesInternal", value = "GRList"): ...

.tags

signature(object = "genomicProfilesInternal"): ...

.tags<-

signature(object = "genomicProfilesInternal", value = "character"): ...

averageExpPWMScore

signature(object = "genomicProfilesInternal"): ...

BPFrequency

signature(object = "genomicProfilesInternal"): ...

BPFrequency<-

signature(object = "genomicProfilesInternal", value = "DNAStringSet"): ...

BPFrequency<-

signature(object = "genomicProfilesInternal", value = "vector"): ...

DNASequenceLength

signature(object = "genomicProfilesInternal"): ...

drop

signature(object = "genomicProfilesInternal"): ...

maxPWMScore

signature(object = "genomicProfilesInternal"): ...

minPWMScore

signature(object = "genomicProfilesInternal"): ...

PFMFormat

signature(object = "genomicProfilesInternal"): ...

PFMFormat<-

signature(object = "genomicProfilesInternal", value = "character"): ...

PositionFrequencyMatrix

signature(object = "genomicProfilesInternal"): ...

PositionFrequencyMatrix<-

signature(object = "genomicProfilesInternal", value = "character"): ...

PositionFrequencyMatrix<-

signature(object = "genomicProfilesInternal", value = "matrix"): ...

PositionWeightMatrix

signature(object = "genomicProfilesInternal"): ...

PositionWeightMatrix<-

signature(object = "genomicProfilesInternal", value = "matrix"): ...

profiles

signature(object = "genomicProfilesInternal"): ...

Author(s)

Patrick C. N. Martin <[e-mail]>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

See Also

genomicProfiles

parameterOptions

Examples

showClass("genomicProfilesInternal")

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.