strandRule_-: Setter method for the 'strandRule' slot in a...

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

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 <[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.

Examples

# Loading data
data(ChIPanalyserData)

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

patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.