genomicProfilesInternal-class {ChIPanalyser} | R Documentation

## 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 <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

    showClass("genomicProfilesInternal")

[Package ChIPanalyser version 1.8.0 Index]