stepSize<- {ChIPanalyser}R Documentation

Setter Method for the stepSize slot in a occupancyProfileParameters

Description

Setter Method for the stepSize slot in a occupancyProfileParameters

Usage

stepSize(object) <- value

Arguments

object

object is a occupancyProfileParameters object

value

value is a positive numeric value that will be assigned to the stepSize slot in a occupancyProfileParameters object. Default is set at 10 base pairs.

Details

It possible to restrict the size of the ChIP-seq-like profile produced by computeChipProfile. Instead of returning ChIP-seq like score for each base pair, it is possible to skip base pairs and only return the predicted enrichement score for every "n" base pair (n is the value assigned to stepSize). This will reduce the size of the output data (unless step size is very large, this will not affect the accuracy of the model). Default is set at 10 base pairs.

Value

Returns a occupancyProfileParameters object with an updated value for the stepSize slot.

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

# Building occupancyProfileParameters object
OPP <- occupancyProfileParameters()
#Setting new Value for maxSignal
stepSize(OPP) <- 20


[Package ChIPanalyser version 1.6.0 Index]