PWMThreshold: Accessor method for the 'PWMThreshold' slot in a...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Accessor method for the PWMThreshold slot in a parameterOptions object

1	PWMThreshold(object)

object

object is a parameterOptions object

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.

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

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<e2><80><93>94.

# Loading data
data(ChIPanalyserData)

#Building data objects
GPP <- parameterOptions(PWMThreshold=0.7)
#Accessing Value for  PWMThreshold
PWMThreshold(GPP)