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

whichstrand

R Documentation

Accessor method for the `whichstrand` slot in a `parameterOptions` object

Description

Accessor method for the whichstrand slot in a parameterOptions object

Usage

whichstrand(object)

Arguments

object

object is a parameterOptions object

Details

PWM Score may be computed on either the positive strand ("+"), the negative strand ("-") or on both strands ("+-").

Value

Returns on which strand PWM Scores should be computed ( whichstrand in a parameterOptions 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. 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( whichstrand="+-")
#Setting New Value for whichstrand
whichstrand(GPP)

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