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

Description Usage Arguments Details Value Author(s) References Examples

Setter method for the strandRule slot in a parameterOptions object.

1	strandRule(object) <- value

`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’

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’

Returns a parameterOptions object with an updated value for the strandRule slot

Patrick C. N. Martin <pm16057@essex.ac.uk>

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84<e2><80><93>94.

# Loading data
data(ChIPanalyserData)

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