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

strandRule<-

R Documentation

Setter method for the `strandRule` slot in a `parameterOptions` object.

Description

Setter method for the strandRule slot in a parameterOptions object.

Usage

strandRule(object) <- value

Arguments

`object`	`object` is a `parameterOptions` object
`value`	`value` is a character string and can be one of the following ‘mean’, ‘max’, ‘sum’. This will only apply if `whichstrand` is ‘+-’. Default set at ‘max’

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 a parameterOptions object with an updated value for the strandRule 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(strandRule="max")
#Setting New Value for strandRule
strandRule(GPP) <- "mean"

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