| AllSitesAboveThreshold {ChIPanalyser} | R Documentation |
AllSitesAboveThreshold slot in a
genomicProfileParameters object.
Extract or Access AllSitesAboveThreshold slot in
genomicProfileParameters object.
AllSitesAboveThreshold(object)
object |
|
As a general rule, AllSitesAboveThreshold is computed and updated
internally in computePWMScore, computeOccupancy,
computeChipProfile. Idealy, this slot should not be updated
by user. There are three differenrent occurances of this slot.
As a GRanges, AllSitesAboveThreshold represents the sites
of one locus that are above PWMThreshold.
As a GRangesList, AllSitesAboveThreshold represents the
sites of multiple loci that are above PWMThreshold.
As a list, AllSitesAboveThreshold represents a list of
GRanges or GRangesList (as described above).
When computing occupancy computeOccupancy, it is possible to
use mutliple values of ScalingFactorPWM and
boundMolecules.
Each element in the list reprensent a combination of
ScalingFactorPWM and boundMolecules.
The specific combination of each element
can be found by using names of AllSitesAboveThreshold
or by using ScalingFactorPWM and boundMolecules.
Returns a GRanges , GRangesList or list containing
containing sites with a Position Weight Matrix Score
above a PWMThreshold.
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, 84–94.
# 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
AllSitesAboveThreshold(GPP)
## Note this slot is now empty as nothing has yet been computed