Accessor method for the PWMThreshold slot in a genomicProfileParameters object

Description

Accessor method for the PWMThreshold slot in a genomicProfileParameters object

Usage

PWMThreshold(object)

Arguments

Details

The computePWMScore function requires a so-called PWM Threshold. This threshold represents the Threshold at which PWM Score should be selected. The PWMThreshold is a positive numeric value (between 0 and 1. If set at 0, all sites will be selected. If set at 0.7 (Default value), then 70 % of PWM Score (and by extension binding sites) will be IGNORED. The top 30 % will be selected.

Value

Returns the value assinged to the PWMThreshold slot in a genomicProfileParameters object

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

# Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#Building data objects
GPP <- genomicProfileParameters(PFM=PFM, PWMThreshold=0.7)
#Accessing Value for  PWMThreshold
PWMThreshold(GPP)