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