averageExpPWMScore: Accessor for 'averageExpPWMScore' slot in a 'genomicProfiles'...
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

averageExpPWMScore

R Documentation

Accessor for `averageExpPWMScore` slot in a `genomicProfiles` object.

Description

Extract or Access averageExpPWMScore slot in a genomicProfiles

Usage

averageExpPWMScore(object)

Arguments

object

object is a genomicProfiles

Details

As a general rule, averageExpPWMScore is computed and updated internally by computeGenomeWideScores. 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 computeGenomeWideScores).

Value

Returns the averageExpPWMScore of a genomicProfiles when computed.

Author(s)

Patrick C.N. Martin <pcnmartin@gmail.com>

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"),"BEAF-32.pfm")
# Building genomicProfiles object
GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR")
# Extracting AllSitesAboveThreshold slot
averageExpPWMScore(GPP)

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

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