averageExpPWMScore | R Documentation |
averageExpPWMScore
slot in a
genomicProfiles
object.
Extract or Access averageExpPWMScore
slot in a
genomicProfiles
averageExpPWMScore(object)
object |
|
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 <pcnmartin@gmail.com>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
# 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
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