strandRule: Accessor Method for the 'strandRule' slot in a...

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Accessor Method for the strandRule slot in a parameterOptions object

Description

Accessor Method for the strandRule slot in a parameterOptions object

Usage

strandRule(object)

Arguments

object

object is a parameterOptions object

Details

When computing the PWM Scores and if whichstrand is set to "+-", strandRule will determine how to handle both strands ( one of three options : "mean", "max", "sum"). If set to "mean", the average PWM Score of both strand will be computed. If set to "max", the highest PWM score between each strand will be selected and finally "sum" will sum both score together. Default set at "max"

Value

Returns the value assigned to strandRule slot (one of three options : "mean", "max", "sum") in a parameterOptions object

Author(s)

Patrick C. N. Martin <[e-mail]>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

Examples

# Loading data
data(ChIPanalyserData)

#Building data objects
GPP <- parameterOptions( strandRule="max")
#Accesssing Value for strandRule
strandRule(GPP)

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.