Accessor Method for the PWM slot in a genomicProfileParameters object

Description

Accessor Method for the PWM slot in a genomicProfileParameters object

Usage

PositionWeightMatrix(object)

Arguments

Details

After creating a genomicProfileParameters 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 <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.

Examples

#Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#Building genomicProfileParameters object
GPP<-genomicProfileParameters(PFM=PFM)
# Accessing Slot
PositionWeightMatrix(GPP)