Accessor for averageExpPWMScore slot in a genomicProfileParameters object.

Description

Extract or Access averageExpPWMScore slot in a genomicProfileParameters

Usage

averageExpPWMScore(object)

Arguments

Details

As a general rule, averageExpPWMScore is computed and updated internally by computeGenomeWidePWMScore. Idealy, this slot should not be updated by user. The averageExpPWMScore is the sum of the exponential of every PWM score for a given DNA sequence and divided by the length of the said DNA sequence (DNASequenceLength). This can either be the full length sequence or only the accessible sequence (see computeGenomeWidePWMScore).

Value

Returns the averageExpPWMScore of a genomicProfileParameters when computed.

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

# Accessing Data
data(ChIPanalyserData)
# path to Position Frequency Matrix
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
# Building genomicProfileParameters object
GPP <- genomicProfileParameters(PFM=PFM)
# Extracting AllSitesAboveThreshold slot
averageExpPWMScore(GPP)

## Note this slot is now empty as nothing has yet been computed