PositionWeightMatrix: Accessor Method for the 'PWM' slot in a 'genomicProfiles'...

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

Accessor Method for the PWM slot in a genomicProfiles object

Description

Accessor Method for the PWM slot in a genomicProfiles object

Usage

PositionWeightMatrix(object)

Arguments

object

object is a genomicProfiles

Details

After creating a genomicProfiles object, it is possible to access the Position Weight Matrix stored in this slot. This slot should always contain something. This slot is either supplied by user or directly computed from a Position Frequency Matrix when supplied.

Value

Returns a matrix in the form of a Position Weight Matrix

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
PositionWeightMatrix(GPP)

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