Accessor method for the PFM slot in a genomicProfileParameters object

Description

Accessor method for the PFM slot in a genomicProfileParameters object

Usage

PositionFrequencyMatrix(object)

Arguments

Details

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

Value

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

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
PositionFrequencyMatrix(GPP)