AllSitesAboveThreshold {ChIPanalyser}R Documentation

Accessor for AllSitesAboveThreshold slot in a genomicProfileParameters object.

Description

Extract or Access AllSitesAboveThreshold slot in genomicProfileParameters object.

Usage

AllSitesAboveThreshold(object)

Arguments

object

genomicProfileParameters object.

Details

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.

Value

Returns a GRanges , GRangesList or list containing containing sites with a Position Weight Matrix Score above a PWMThreshold.

Author(s)

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

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"),"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

[Package ChIPanalyser version 1.4.0 Index]