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

Description Usage Arguments Details Value Author(s) References Examples

Extract or Access averageExpPWMScore slot in a genomicProfiles

1	averageExpPWMScore(object)

object

object is a genomicProfiles

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).

Returns the averageExpPWMScore of a genomicProfiles when computed.

Patrick C.N. Martin <pm16057@essex.ac.uk>

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.

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

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