PositionFrequencyMatrix: Accessor method for the 'PFM' slot in a 'genomicProfiles'...

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

Accessor method for the PFM slot in a genomicProfiles object

Description

Accessor method for the PFM slot in a genomicProfiles object

Usage

PositionFrequencyMatrix(object)

Arguments

object

object is a genomicProfiles object

Details

After creating a genomicProfiles object, it is possible to access the Position Frequency Matrix slot. However this slot will be empty if the genomicProfiles object was built using directly a Position Weight Matrix. See genomicProfiles

Value

Returns the Position Frequency Matrix (PFM slot) used to compute the PositionWeightMatrix in a genomicProfiles object

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.

Examples

#Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BEAF-32.pfm")
#Building genomicProfiles object
GPP<-genomicProfiles(PFM=PFM,PFMFormat="JASPAR")
# Accessing Slot
PositionFrequencyMatrix(GPP)

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