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

Description Usage Arguments Details Value Author(s) References Examples

Description

Accessor method for the PFM slot in a genomicProfiles object

Usage

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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 <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<e2><80><93>94.

Examples

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

ChIPanalyser documentation built on Nov. 8, 2020, 8:23 p.m.