genomicProfilesInternal-class: Class '"genomicProfilesInternal"'

Description Objects from the Class Slots Methods Author(s) References See Also Examples

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 <pm16057@essex.ac.uk>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

See Also

genomicProfiles

parameterOptions

Examples

1
showClass("genomicProfilesInternal")

patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.