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

whichstrand<-

R Documentation

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

Description

Setter method for the whichstrand slot in a parameterOptions object

Usage

whichstrand(object) <- value

Arguments

`object`	`object` is a `parameterOptions` object
`value`	`value` is a character string specifying which strand should be used to compute PWM Scores. The three available options are the following: "+","-" or "+-". Default is "+-"

Details

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

Value

Returns a parameterOptions object with an updated value for the whichstrand 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. 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.